diff --git a/docs/changes/newsfragments/6942.breaking b/docs/changes/newsfragments/6942.breaking
new file mode 100644
index 000000000000..b5a5bdcab12b
--- /dev/null
+++ b/docs/changes/newsfragments/6942.breaking
@@ -0,0 +1,4 @@
+The QCoDeS dataset sqlite connection class `ConnectionPlus` has been deprecated and replace with `AtomicConnection`.
+Unlike `ConnectionPlus` `AtomicConnection` is a direct subclass of `sqlite3.Connection` which enables better type checking
+and will allow QCoDeS to drop the dependency on `wrapt`. The function `make_connection_plus_from` is also deprecated and
+it is no longer supported to convert a connection from a sqlite3 connection to a QCoDeS specific connection.
diff --git a/pyproject.toml b/pyproject.toml
index 1350cbac386d..381f608f3bb2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -239,7 +239,9 @@ filterwarnings = [
     'ignore:open_binary is deprecated:DeprecationWarning', # pyvisa-sim
     'ignore:Jupyter is migrating its paths to use standard platformdirs:DeprecationWarning', # jupyter
     'ignore:Parsing dates involving a day of month without a year specified is ambiguious:DeprecationWarning', # ipykernel 3.13+
-    'ignore:unclosed database in:ResourceWarning' # internal should be fixed
+    'ignore:unclosed database in:ResourceWarning', # internal should be fixed
+    'ignore:ConnectionPlus is deprecated:qcodes.utils.deprecate.QCoDeSDeprecationWarning',  # remove once deprecated ConnectionPlus has been removed
+    'ignore:make_connection_plus_from is deprecated:qcodes.utils.deprecate.QCoDeSDeprecationWarning',  # remove once deprecated ConnectionPlus has been removed
 ]
 
 [tool.ruff]
diff --git a/src/qcodes/dataset/__init__.py b/src/qcodes/dataset/__init__.py
index a46957714493..999d5ce4a6ac 100644
--- a/src/qcodes/dataset/__init__.py
+++ b/src/qcodes/dataset/__init__.py
@@ -44,7 +44,10 @@
 )
 from .measurements import Measurement
 from .plotting import plot_by_id, plot_dataset
-from .sqlite.connection import ConnectionPlus
+from .sqlite.connection import (
+    AtomicConnection,
+    ConnectionPlus,  # pyright: ignore[reportDeprecated]
+)
 from .sqlite.database import (
     connect,
     initialise_database,
@@ -61,6 +64,7 @@
 __all__ = [
     "AbstractSweep",
     "ArraySweep",
+    "AtomicConnection",
     "BreakConditionInterrupt",
     "ConnectionPlus",
     "DataSetDefinition",
diff --git a/src/qcodes/dataset/data_set.py b/src/qcodes/dataset/data_set.py
index d67290a687ec..c5efd9772efd 100644
--- a/src/qcodes/dataset/data_set.py
+++ b/src/qcodes/dataset/data_set.py
@@ -35,7 +35,11 @@
 )
 from qcodes.dataset.guids import filter_guids_by_parts, generate_guid, parse_guid
 from qcodes.dataset.linked_datasets.links import Link, links_to_str, str_to_links
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic, atomic_transaction
+from qcodes.dataset.sqlite.connection import (
+    AtomicConnection,
+    atomic,
+    atomic_transaction,
+)
 from qcodes.dataset.sqlite.database import (
     conn_from_dbpath_or_conn,
     connect,
@@ -128,7 +132,7 @@ class _BackgroundWriter(Thread):
     Write the results from the DataSet's dataqueue in a new thread
     """
 
-    def __init__(self, queue: Queue[Any], conn: ConnectionPlus):
+    def __init__(self, queue: Queue[Any], conn: AtomicConnection):
         super().__init__(daemon=True)
         self.queue = queue
         self.path = conn.path_to_dbfile
@@ -206,7 +210,7 @@ def __init__(
         self,
         path_to_db: str | None = None,
         run_id: int | None = None,
-        conn: ConnectionPlus | None = None,
+        conn: AtomicConnection | None = None,
         exp_id: int | None = None,
         name: str | None = None,
         specs: SpecsOrInterDeps | None = None,
@@ -1556,7 +1560,7 @@ def load_by_run_spec(
     sample_id: int | None = None,
     location: int | None = None,
     work_station: int | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
 ) -> DataSetProtocol:
     """
     Load a run from one or more pieces of runs specification. All
@@ -1635,7 +1639,7 @@ def get_guids_by_run_spec(
     sample_id: int | None = None,
     location: int | None = None,
     work_station: int | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
 ) -> list[str]:
     """
     Get a list of matching guids from one or more pieces of runs specification. All
@@ -1677,7 +1681,7 @@ def get_guids_by_run_spec(
     return matched_guids
 
 
-def load_by_id(run_id: int, conn: ConnectionPlus | None = None) -> DataSetProtocol:
+def load_by_id(run_id: int, conn: AtomicConnection | None = None) -> DataSetProtocol:
     """
     Load a dataset by run id
 
@@ -1723,7 +1727,7 @@ def load_by_id(run_id: int, conn: ConnectionPlus | None = None) -> DataSetProtoc
     return d
 
 
-def load_by_guid(guid: str, conn: ConnectionPlus | None = None) -> DataSetProtocol:
+def load_by_guid(guid: str, conn: AtomicConnection | None = None) -> DataSetProtocol:
     """
     Load a dataset by its GUID
 
@@ -1763,7 +1767,7 @@ def load_by_guid(guid: str, conn: ConnectionPlus | None = None) -> DataSetProtoc
 
 
 def load_by_counter(
-    counter: int, exp_id: int, conn: ConnectionPlus | None = None
+    counter: int, exp_id: int, conn: AtomicConnection | None = None
 ) -> DataSetProtocol:
     """
     Load a dataset given its counter in a given experiment
@@ -1807,7 +1811,9 @@ def load_by_counter(
     return d
 
 
-def _get_datasetprotocol_from_guid(guid: str, conn: ConnectionPlus) -> DataSetProtocol:
+def _get_datasetprotocol_from_guid(
+    guid: str, conn: AtomicConnection
+) -> DataSetProtocol:
     run_id = get_runid_from_guid(conn, guid)
     if run_id is None:
         raise NameError(
@@ -1840,7 +1846,7 @@ def _get_datasetprotocol_from_guid(guid: str, conn: ConnectionPlus) -> DataSetPr
     return d
 
 
-def _get_datasetprotocol_export_info(run_id: int, conn: ConnectionPlus) -> ExportInfo:
+def _get_datasetprotocol_export_info(run_id: int, conn: AtomicConnection) -> ExportInfo:
     metadata = get_metadata_from_run_id(conn=conn, run_id=run_id)
     export_info_str = metadata.get("export_info", "")
     export_info = ExportInfo.from_str(export_info_str)
@@ -1853,7 +1859,7 @@ def new_data_set(
     specs: SPECS | None = None,
     values: VALUES | None = None,
     metadata: Any | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
     in_memory_cache: bool = True,
 ) -> DataSet:
     """
@@ -1894,7 +1900,7 @@ def new_data_set(
 
 
 def generate_dataset_table(
-    guids: Sequence[str], conn: ConnectionPlus | None = None
+    guids: Sequence[str], conn: AtomicConnection | None = None
 ) -> str:
     """
     Generate an ASCII art table of information about the runs attached to the
@@ -1902,7 +1908,7 @@ def generate_dataset_table(
 
     Args:
         guids: Sequence of one or more guids
-        conn: A ConnectionPlus object with a connection to the database.
+        conn: An AtomicConnection object with a connection to the database.
 
     Returns: ASCII art table of information about the supplied guids.
 
diff --git a/src/qcodes/dataset/data_set_cache.py b/src/qcodes/dataset/data_set_cache.py
index b9948c1e4f9b..80d57ad4c0a6 100644
--- a/src/qcodes/dataset/data_set_cache.py
+++ b/src/qcodes/dataset/data_set_cache.py
@@ -25,7 +25,7 @@
     import xarray as xr
 
     from qcodes.dataset.descriptions.rundescriber import RunDescriber
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
 
     # used in forward refs that cannot be detected
     from .data_set import DataSet  # noqa F401
@@ -201,7 +201,7 @@ def to_xarray_dataset(
 
 
 def load_new_data_from_db_and_append(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table_name: str,
     rundescriber: RunDescriber,
     write_status: Mapping[str, int | None],
diff --git a/src/qcodes/dataset/data_set_in_memory.py b/src/qcodes/dataset/data_set_in_memory.py
index 347cf86fd30c..bed5d709c0c8 100644
--- a/src/qcodes/dataset/data_set_in_memory.py
+++ b/src/qcodes/dataset/data_set_in_memory.py
@@ -23,7 +23,7 @@
 from qcodes.dataset.export_config import DataExportType
 from qcodes.dataset.guids import generate_guid
 from qcodes.dataset.linked_datasets.links import Link, links_to_str
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic
 from qcodes.dataset.sqlite.database import conn_from_dbpath_or_conn
 from qcodes.dataset.sqlite.queries import (
     RUNS_TABLE_COLUMNS,
@@ -302,7 +302,7 @@ def _load_from_netcdf(
         return ds
 
     @classmethod
-    def _load_from_db(cls, conn: ConnectionPlus, guid: str) -> DataSetInMem:
+    def _load_from_db(cls, conn: AtomicConnection, guid: str) -> DataSetInMem:
         run_attributes = get_raw_run_attributes(conn, guid)
         if run_attributes is None:
             raise RuntimeError(
diff --git a/src/qcodes/dataset/data_set_info.py b/src/qcodes/dataset/data_set_info.py
index 3483b4631d7a..b79faffef9a5 100644
--- a/src/qcodes/dataset/data_set_info.py
+++ b/src/qcodes/dataset/data_set_info.py
@@ -16,7 +16,7 @@
 
 if TYPE_CHECKING:
     from qcodes.dataset.descriptions.rundescriber import RunDescriber
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
 
 
 class RunAttributesDict(TypedDict):
@@ -34,7 +34,7 @@ class RunAttributesDict(TypedDict):
     snapshot: dict[str, Any] | None
 
 
-def get_run_attributes(conn: ConnectionPlus, guid: str) -> RunAttributesDict | None:
+def get_run_attributes(conn: AtomicConnection, guid: str) -> RunAttributesDict | None:
     """
     Look up all information and metadata about a given dataset captured
     in the database.
diff --git a/src/qcodes/dataset/database_extract_runs.py b/src/qcodes/dataset/database_extract_runs.py
index a2a39f9ac4e6..045940185ecf 100644
--- a/src/qcodes/dataset/database_extract_runs.py
+++ b/src/qcodes/dataset/database_extract_runs.py
@@ -9,7 +9,7 @@
 from qcodes.dataset.data_set import DataSet
 from qcodes.dataset.dataset_helpers import _add_run_to_runs_table
 from qcodes.dataset.experiment_container import _create_exp_if_needed
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic
 from qcodes.dataset.sqlite.database import (
     connect,
     get_db_version_and_newest_available_version,
@@ -128,7 +128,7 @@ def extract_runs_into_db(
 
 
 def _extract_single_dataset_into_db(
-    dataset: DataSet, target_conn: ConnectionPlus, target_exp_id: int
+    dataset: DataSet, target_conn: AtomicConnection, target_exp_id: int
 ) -> None:
     """
     NB: This function should only be called from within
diff --git a/src/qcodes/dataset/database_fix_functions.py b/src/qcodes/dataset/database_fix_functions.py
index 404f977e35a2..bbcbb63750c4 100644
--- a/src/qcodes/dataset/database_fix_functions.py
+++ b/src/qcodes/dataset/database_fix_functions.py
@@ -15,7 +15,11 @@
 from qcodes.dataset.descriptions.rundescriber import RunDescriber
 from qcodes.dataset.descriptions.versioning import v0
 from qcodes.dataset.descriptions.versioning.converters import old_to_new
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic, atomic_transaction
+from qcodes.dataset.sqlite.connection import (
+    AtomicConnection,
+    atomic,
+    atomic_transaction,
+)
 from qcodes.dataset.sqlite.db_upgrades.version import get_user_version
 from qcodes.dataset.sqlite.queries import (
     _get_parameters,
@@ -35,7 +39,7 @@
 log = logging.getLogger(__name__)
 
 
-def fix_version_4a_run_description_bug(conn: ConnectionPlus) -> dict[str, int]:
+def fix_version_4a_run_description_bug(conn: AtomicConnection) -> dict[str, int]:
     """
     Fix function to fix a bug where the RunDescriber accidentally wrote itself
     to string using the (new) InterDependencies_ object instead of the (old)
@@ -124,7 +128,7 @@ def _convert_run_describer_v1_like_dict_to_v0_like_dict(
     return old_desc_dict
 
 
-def fix_wrong_run_descriptions(conn: ConnectionPlus, run_ids: Sequence[int]) -> None:
+def fix_wrong_run_descriptions(conn: AtomicConnection, run_ids: Sequence[int]) -> None:
     """
     NB: This is a FIX function. Do not use it unless your database has been
     diagnosed with the problem that this function fixes.
diff --git a/src/qcodes/dataset/dataset_helpers.py b/src/qcodes/dataset/dataset_helpers.py
index 9388abdf8188..5cb11a13f0d4 100644
--- a/src/qcodes/dataset/dataset_helpers.py
+++ b/src/qcodes/dataset/dataset_helpers.py
@@ -11,12 +11,12 @@
 
 if TYPE_CHECKING:
     from qcodes.dataset.data_set_protocol import DataSetProtocol
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
 
 
 def _add_run_to_runs_table(
     dataset: DataSetProtocol,
-    target_conn: ConnectionPlus,
+    target_conn: AtomicConnection,
     target_exp_id: int,
     create_run_table: bool = True,
 ) -> tuple[int, int, str | None]:
diff --git a/src/qcodes/dataset/experiment_container.py b/src/qcodes/dataset/experiment_container.py
index 939e44fb3633..ad1f658e4a3c 100644
--- a/src/qcodes/dataset/experiment_container.py
+++ b/src/qcodes/dataset/experiment_container.py
@@ -7,7 +7,7 @@
 
 from qcodes.dataset.data_set import DataSet, load_by_id, new_data_set
 from qcodes.dataset.experiment_settings import _set_default_experiment_id
-from qcodes.dataset.sqlite.connection import ConnectionPlus, path_to_dbfile
+from qcodes.dataset.sqlite.connection import AtomicConnection, path_to_dbfile
 from qcodes.dataset.sqlite.database import (
     conn_from_dbpath_or_conn,
     connect,
@@ -42,7 +42,7 @@ def __init__(
         name: str | None = None,
         sample_name: str | None = None,
         format_string: str = "{}-{}-{}",
-        conn: ConnectionPlus | None = None,
+        conn: AtomicConnection | None = None,
     ) -> None:
         """
         Create or load an experiment. If exp_id is None, a new experiment is
@@ -207,7 +207,7 @@ def __repr__(self) -> str:
 # public api
 
 
-def experiments(conn: ConnectionPlus | None = None) -> list[Experiment]:
+def experiments(conn: AtomicConnection | None = None) -> list[Experiment]:
     """
     List all the experiments in the container (database file from config)
 
@@ -228,7 +228,7 @@ def new_experiment(
     name: str,
     sample_name: str | None,
     format_string: str = "{}-{}-{}",
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
 ) -> Experiment:
     """
     Create a new experiment (in the database file from config)
@@ -259,7 +259,7 @@ def new_experiment(
     return experiment
 
 
-def load_experiment(exp_id: int, conn: ConnectionPlus | None = None) -> Experiment:
+def load_experiment(exp_id: int, conn: AtomicConnection | None = None) -> Experiment:
     """
     Load experiment with the specified id (from database file from config)
 
@@ -304,7 +304,7 @@ def load_last_experiment() -> Experiment:
 def load_experiment_by_name(
     name: str,
     sample: str | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
     load_last_duplicate: bool = False,
 ) -> Experiment:
     """
@@ -365,7 +365,7 @@ def load_experiment_by_name(
 def load_or_create_experiment(
     experiment_name: str,
     sample_name: str | None = None,
-    conn: ConnectionPlus | None = None,
+    conn: AtomicConnection | None = None,
     load_last_duplicate: bool = False,
 ) -> Experiment:
     """
@@ -405,7 +405,7 @@ def load_or_create_experiment(
 
 
 def _create_exp_if_needed(
-    target_conn: ConnectionPlus,
+    target_conn: AtomicConnection,
     exp_name: str,
     sample_name: str,
     fmt_str: str,
diff --git a/src/qcodes/dataset/experiment_settings.py b/src/qcodes/dataset/experiment_settings.py
index 00da1c178b83..d1b6c1cb8d06 100644
--- a/src/qcodes/dataset/experiment_settings.py
+++ b/src/qcodes/dataset/experiment_settings.py
@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from qcodes.dataset.sqlite.connection import ConnectionPlus, path_to_dbfile
+from qcodes.dataset.sqlite.connection import AtomicConnection, path_to_dbfile
 from qcodes.dataset.sqlite.queries import get_last_experiment
 
 _default_experiment: dict[str, int | None] = {}
@@ -38,7 +38,7 @@ def _get_latest_default_experiment_id(db_path: str) -> int | None:
     return _default_experiment.get(db_path, None)
 
 
-def reset_default_experiment_id(conn: ConnectionPlus | None = None) -> None:
+def reset_default_experiment_id(conn: AtomicConnection | None = None) -> None:
     """
     Resets the default experiment id to to the last experiment in the db.
     """
@@ -50,7 +50,7 @@ def reset_default_experiment_id(conn: ConnectionPlus | None = None) -> None:
         _default_experiment[db_path] = None
 
 
-def get_default_experiment_id(conn: ConnectionPlus) -> int:
+def get_default_experiment_id(conn: AtomicConnection) -> int:
     """
     Returns the latest created/ loaded experiment's exp_id as the default
     experiment. If it is not set the maximum exp_id returned as the default.
diff --git a/src/qcodes/dataset/measurements.py b/src/qcodes/dataset/measurements.py
index e04a0cceed20..9d0c24effe01 100644
--- a/src/qcodes/dataset/measurements.py
+++ b/src/qcodes/dataset/measurements.py
@@ -59,7 +59,7 @@
 
     from qcodes.dataset.descriptions.versioning.rundescribertypes import Shapes
     from qcodes.dataset.experiment_container import Experiment
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
     from qcodes.dataset.sqlite.query_helpers import VALUE
 
 log = logging.getLogger(__name__)
@@ -631,7 +631,7 @@ def __enter__(self) -> DataSaver:
         if self.experiment is not None:
             exp_id: int | None = self.experiment.exp_id
             path_to_db: str | None = self.experiment.path_to_db
-            conn: ConnectionPlus | None = self.experiment.conn
+            conn: AtomicConnection | None = self.experiment.conn
         else:
             exp_id = None
             path_to_db = None
diff --git a/src/qcodes/dataset/sqlite/connection.py b/src/qcodes/dataset/sqlite/connection.py
index c469c806d477..2e82099dbfaa 100644
--- a/src/qcodes/dataset/sqlite/connection.py
+++ b/src/qcodes/dataset/sqlite/connection.py
@@ -7,22 +7,29 @@
 from __future__ import annotations
 
 import logging
+import sqlite3
 from contextlib import contextmanager
 from typing import TYPE_CHECKING, Any
 
 import wrapt  # type: ignore[import-untyped]
+from typing_extensions import deprecated
 
-from qcodes.utils import DelayedKeyboardInterrupt
+from qcodes.utils import DelayedKeyboardInterrupt, QCoDeSDeprecationWarning
 
 if TYPE_CHECKING:
-    import sqlite3
     from collections.abc import Iterator
 
 log = logging.getLogger(__name__)
 
 
+@deprecated(
+    "ConnectionPlus is deprecated. Please use connect to create an AtomicConnection.",
+    category=QCoDeSDeprecationWarning,
+)
 class ConnectionPlus(wrapt.ObjectProxy):  # pyright: ignore[reportUntypedBaseClass]
     """
+    Note this is a legacy class. Please refer to :class:`AtomicConnection`
+
     A class to extend the sqlite3.Connection object. Since sqlite3.Connection
     has no __dict__, we can not directly add attributes to its instance
     directly.
@@ -48,7 +55,7 @@ class ConnectionPlus(wrapt.ObjectProxy):  # pyright: ignore[reportUntypedBaseCla
     def __init__(self, sqlite3_connection: sqlite3.Connection):
         super().__init__(sqlite3_connection)
 
-        if isinstance(sqlite3_connection, ConnectionPlus):
+        if isinstance(sqlite3_connection, ConnectionPlus):  # pyright: ignore[reportDeprecated]
             raise ValueError(
                 "Attempted to create `ConnectionPlus` from a "
                 "`ConnectionPlus` object which is not allowed."
@@ -57,9 +64,39 @@ def __init__(self, sqlite3_connection: sqlite3.Connection):
         self.path_to_dbfile = path_to_dbfile(sqlite3_connection)
 
 
+class AtomicConnection(sqlite3.Connection):
+    """
+    A class to extend the sqlite3.Connection object. This extends
+    Connection to allow addition operations to be performed atomically.
+
+    It is recommended to create an AtomicConnection using the function :func:`connect`
+
+    """
+
+    atomic_in_progress: bool = False
+    """
+    a bool describing whether the connection is
+    currently in the middle of an atomic block of transactions, thus
+    allowing to nest `atomic` context managers
+    """
+    path_to_dbfile: str = ""
+    """
+    Path to the database file of the connection.
+    """
+
+    def __init__(self, *args: Any, **kwargs: Any) -> None:
+        super().__init__(*args, **kwargs)
+
+        self.path_to_dbfile = path_to_dbfile(self)
+
+
+@deprecated(
+    "make_connection_plus_from is deprecated. Please use connect to create an AtomicConnection",
+    category=QCoDeSDeprecationWarning,
+)
 def make_connection_plus_from(
-    conn: sqlite3.Connection | ConnectionPlus,
-) -> ConnectionPlus:
+    conn: sqlite3.Connection | ConnectionPlus,  # pyright: ignore[reportDeprecated]
+) -> ConnectionPlus:  # pyright: ignore[reportDeprecated]
     """
     Makes a ConnectionPlus connection object out of a given argument.
 
@@ -73,15 +110,15 @@ def make_connection_plus_from(
         the "same" connection but as ConnectionPlus object
 
     """
-    if not isinstance(conn, ConnectionPlus):
-        conn_plus = ConnectionPlus(conn)
+    if not isinstance(conn, ConnectionPlus):  # pyright: ignore[reportDeprecated]
+        conn_plus = ConnectionPlus(conn)  # pyright: ignore[reportDeprecated]
     else:
         conn_plus = conn
     return conn_plus
 
 
 @contextmanager
-def atomic(conn: ConnectionPlus) -> Iterator[ConnectionPlus]:
+def atomic(conn: AtomicConnection) -> Iterator[AtomicConnection]:
     """
     Guard a series of transactions as atomic.
 
@@ -97,10 +134,10 @@ def atomic(conn: ConnectionPlus) -> Iterator[ConnectionPlus]:
 
     """
     with DelayedKeyboardInterrupt(context={"reason": "sqlite atomic operation"}):
-        if not isinstance(conn, ConnectionPlus):
+        if not isinstance(conn, ConnectionPlus | AtomicConnection):  # pyright: ignore[reportDeprecated]
             raise ValueError(
                 "atomic context manager only accepts "
-                "ConnectionPlus database connection objects."
+                "AtomicConnection or ConnectionPlus database connection objects."
             )
 
         is_outmost = not (conn.atomic_in_progress)
@@ -135,7 +172,7 @@ def atomic(conn: ConnectionPlus) -> Iterator[ConnectionPlus]:
             conn.atomic_in_progress = old_atomic_in_progress
 
 
-def transaction(conn: ConnectionPlus, sql: str, *args: Any) -> sqlite3.Cursor:
+def transaction(conn: AtomicConnection, sql: str, *args: Any) -> sqlite3.Cursor:
     """Perform a transaction.
     The transaction needs to be committed or rolled back.
 
@@ -157,7 +194,7 @@ def transaction(conn: ConnectionPlus, sql: str, *args: Any) -> sqlite3.Cursor:
     return c
 
 
-def atomic_transaction(conn: ConnectionPlus, sql: str, *args: Any) -> sqlite3.Cursor:
+def atomic_transaction(conn: AtomicConnection, sql: str, *args: Any) -> sqlite3.Cursor:
     """Perform an **atomic** transaction.
     The transaction is committed if there are no exceptions else the
     transaction is rolled back.
@@ -179,7 +216,7 @@ def atomic_transaction(conn: ConnectionPlus, sql: str, *args: Any) -> sqlite3.Cu
     return c
 
 
-def path_to_dbfile(conn: ConnectionPlus | sqlite3.Connection) -> str:
+def path_to_dbfile(conn: AtomicConnection | sqlite3.Connection) -> str:
     """
     Return the path of the database file that the conn object is connected to
     """
diff --git a/src/qcodes/dataset/sqlite/database.py b/src/qcodes/dataset/sqlite/database.py
index a9644ea383ea..b1ea7fc761ee 100644
--- a/src/qcodes/dataset/sqlite/database.py
+++ b/src/qcodes/dataset/sqlite/database.py
@@ -18,7 +18,7 @@
 
 import qcodes
 from qcodes.dataset.experiment_settings import reset_default_experiment_id
-from qcodes.dataset.sqlite.connection import ConnectionPlus
+from qcodes.dataset.sqlite.connection import AtomicConnection
 from qcodes.dataset.sqlite.db_upgrades import (
     _latest_available_version,
     perform_db_upgrade,
@@ -119,7 +119,9 @@ def _adapt_complex(value: complex | np.complexfloating) -> sqlite3.Binary:
     return sqlite3.Binary(out.read())
 
 
-def connect(name: str | Path, debug: bool = False, version: int = -1) -> ConnectionPlus:
+def connect(
+    name: str | Path, debug: bool = False, version: int = -1
+) -> AtomicConnection:
     """
     Connect or create  database. If debug the queries will be echoed back.
     This function takes care of registering the numpy/sqlite type
@@ -133,7 +135,7 @@ def connect(name: str | Path, debug: bool = False, version: int = -1) -> Connect
 
     Returns:
         connection object to the database (note, it is
-        :class:`ConnectionPlus`, not :class:`sqlite3.Connection`)
+        :class:`AtomicConnection`, which is a subclass of :class:`sqlite3.Connection`)
 
     """
     # register numpy->binary(TEXT) adapter
@@ -141,10 +143,12 @@ def connect(name: str | Path, debug: bool = False, version: int = -1) -> Connect
     # register binary(TEXT) -> numpy converter
     sqlite3.register_converter("array", _convert_array)
 
-    sqlite3_conn = sqlite3.connect(
-        name, detect_types=sqlite3.PARSE_DECLTYPES, check_same_thread=True
+    conn = sqlite3.connect(
+        name,
+        detect_types=sqlite3.PARSE_DECLTYPES,
+        check_same_thread=True,
+        factory=AtomicConnection,
     )
-    conn = ConnectionPlus(sqlite3_conn)
 
     latest_supported_version = _latest_available_version()
     db_version = get_user_version(conn)
@@ -232,7 +236,7 @@ def initialise_database(journal_mode: JournalMode | None = "WAL") -> None:
     del conn
 
 
-def set_journal_mode(conn: ConnectionPlus, journal_mode: JournalMode) -> None:
+def set_journal_mode(conn: AtomicConnection, journal_mode: JournalMode) -> None:
     """
     Set the ``atomic commit and rollback mode`` of the sqlite database.
     See https://www.sqlite.org/pragma.html#pragma_journal_mode for details.
@@ -291,20 +295,20 @@ def initialised_database_at(db_file_with_abs_path: str | Path) -> Iterator[None]
 
 
 def conn_from_dbpath_or_conn(
-    conn: ConnectionPlus | None, path_to_db: str | Path | None
-) -> ConnectionPlus:
+    conn: AtomicConnection | None, path_to_db: str | Path | None
+) -> AtomicConnection:
     """
     A small helper function to abstract the logic needed for functions
-    that take either a `ConnectionPlus` or the path to a db file.
+    that take either an `AtomicConnection` or the path to a db file.
     If neither is given this will fall back to the default db location.
     It is an error to supply both.
 
     Args:
-        conn: A ConnectionPlus object pointing to a sqlite database
+        conn: A AtomicConnection object pointing to a sqlite database
         path_to_db: The path to a db file.
 
     Returns:
-        A `ConnectionPlus` object
+        A `AtomicConnection` object
 
     """
 
diff --git a/src/qcodes/dataset/sqlite/db_upgrades/__init__.py b/src/qcodes/dataset/sqlite/db_upgrades/__init__.py
index ce831c21cbd5..3c9000f07377 100644
--- a/src/qcodes/dataset/sqlite/db_upgrades/__init__.py
+++ b/src/qcodes/dataset/sqlite/db_upgrades/__init__.py
@@ -25,7 +25,7 @@
 
 from qcodes.dataset.guids import generate_guid
 from qcodes.dataset.sqlite.connection import (
-    ConnectionPlus,
+    AtomicConnection,
     atomic,
     atomic_transaction,
     transaction,
@@ -41,7 +41,7 @@
 # see https://mypy.readthedocs.io/en/stable/protocols.html#callback-protocols
 class TUpgraderFunction(Protocol):
     def __call__(
-        self, conn: ConnectionPlus, show_progress_bar: bool = True
+        self, conn: AtomicConnection, show_progress_bar: bool = True
     ) -> None: ...
 
     @property
@@ -60,7 +60,7 @@ def _latest_available_version() -> int:
     return len(_UPGRADE_ACTIONS)
 
 
-def _get_no_of_runs(conn: ConnectionPlus) -> int:
+def _get_no_of_runs(conn: AtomicConnection) -> int:
     no_of_runs_query = "SELECT max(run_id) FROM runs"
     no_of_runs = one(atomic_transaction(conn, no_of_runs_query), "max(run_id)")
     no_of_runs = no_of_runs or 0
@@ -72,7 +72,7 @@ def upgrader(func: TUpgraderFunction) -> TUpgraderFunction:
     Decorator for database version upgrade functions. An upgrade function
     must have the name `perform_db_upgrade_N_to_M` where N = M-1. For
     simplicity, an upgrade function must take a single argument of type
-    `ConnectionPlus`. The upgrade function must either perform the upgrade
+    `AtomicConnection`. The upgrade function must either perform the upgrade
     and return (no return values allowed) or fail to perform the upgrade,
     in which case it must raise a RuntimeError. A failed upgrade must be
     completely rolled back before the RuntimeError is raises.
@@ -104,7 +104,7 @@ def upgrader(func: TUpgraderFunction) -> TUpgraderFunction:
         )
 
     @wraps(func)
-    def do_upgrade(conn: ConnectionPlus, show_progress_bar: bool = True) -> None:
+    def do_upgrade(conn: AtomicConnection, show_progress_bar: bool = True) -> None:
         log.info(f"Starting database upgrade version {from_version} to {to_version}")
 
         start_version = get_user_version(conn)
@@ -126,7 +126,7 @@ def do_upgrade(conn: ConnectionPlus, show_progress_bar: bool = True) -> None:
     return do_upgrade
 
 
-def perform_db_upgrade(conn: ConnectionPlus, version: int = -1) -> None:
+def perform_db_upgrade(conn: AtomicConnection, version: int = -1) -> None:
     """
     This is intended to perform all upgrades as needed to bring the
     db from version 0 to the most current version (or the version specified).
@@ -156,7 +156,7 @@ def perform_db_upgrade(conn: ConnectionPlus, version: int = -1) -> None:
 
 @upgrader
 def perform_db_upgrade_0_to_1(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 0 to version 1
@@ -205,7 +205,7 @@ def perform_db_upgrade_0_to_1(
 
 @upgrader
 def perform_db_upgrade_1_to_2(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 1 to version 2
@@ -243,7 +243,7 @@ def perform_db_upgrade_1_to_2(
 
 @upgrader
 def perform_db_upgrade_2_to_3(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 2 to version 3
@@ -260,7 +260,7 @@ def perform_db_upgrade_2_to_3(
 
 @upgrader
 def perform_db_upgrade_3_to_4(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 3 to version 4. This really
@@ -278,7 +278,7 @@ def perform_db_upgrade_3_to_4(
 
 @upgrader
 def perform_db_upgrade_4_to_5(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 4 to version 5.
@@ -299,7 +299,7 @@ def perform_db_upgrade_4_to_5(
 
 @upgrader
 def perform_db_upgrade_5_to_6(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 5 to version 6.
@@ -315,7 +315,7 @@ def perform_db_upgrade_5_to_6(
 
 @upgrader
 def perform_db_upgrade_6_to_7(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 6 to version 7
@@ -352,7 +352,7 @@ def perform_db_upgrade_6_to_7(
 
 @upgrader
 def perform_db_upgrade_7_to_8(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 7 to version 8.
@@ -370,7 +370,7 @@ def perform_db_upgrade_7_to_8(
 
 @upgrader
 def perform_db_upgrade_8_to_9(
-    conn: ConnectionPlus, show_progress_bar: bool = True
+    conn: AtomicConnection, show_progress_bar: bool = True
 ) -> None:
     """
     Perform the upgrade from version 8 to version 9.
diff --git a/src/qcodes/dataset/sqlite/db_upgrades/upgrade_2_to_3.py b/src/qcodes/dataset/sqlite/db_upgrades/upgrade_2_to_3.py
index c3caf4fed984..e51e76e85943 100644
--- a/src/qcodes/dataset/sqlite/db_upgrades/upgrade_2_to_3.py
+++ b/src/qcodes/dataset/sqlite/db_upgrades/upgrade_2_to_3.py
@@ -11,7 +11,7 @@
 from qcodes.dataset.descriptions.param_spec import ParamSpec
 from qcodes.dataset.descriptions.versioning.v0 import InterDependencies
 from qcodes.dataset.sqlite.connection import (
-    ConnectionPlus,
+    AtomicConnection,
     atomic,
     atomic_transaction,
     transaction,
@@ -24,7 +24,7 @@
 log = logging.getLogger(__name__)
 
 
-def _2to3_get_result_tables(conn: ConnectionPlus) -> dict[int, str]:
+def _2to3_get_result_tables(conn: AtomicConnection) -> dict[int, str]:
     rst_query = "SELECT run_id, result_table_name FROM runs"
     cur = conn.cursor()
     cur.execute(rst_query)
@@ -37,7 +37,7 @@ def _2to3_get_result_tables(conn: ConnectionPlus) -> dict[int, str]:
     return results
 
 
-def _2to3_get_layout_ids(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
+def _2to3_get_layout_ids(conn: AtomicConnection) -> defaultdict[int, list[int]]:
     query = """
             select runs.run_id, layouts.layout_id
             FROM layouts
@@ -56,7 +56,7 @@ def _2to3_get_layout_ids(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
     return results
 
 
-def _2to3_get_indeps(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
+def _2to3_get_indeps(conn: AtomicConnection) -> defaultdict[int, list[int]]:
     query = """
             SELECT layouts.run_id, layouts.layout_id
             FROM layouts
@@ -75,7 +75,7 @@ def _2to3_get_indeps(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
     return results
 
 
-def _2to3_get_deps(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
+def _2to3_get_deps(conn: AtomicConnection) -> defaultdict[int, list[int]]:
     query = """
             SELECT layouts.run_id, layouts.layout_id
             FROM layouts
@@ -94,7 +94,7 @@ def _2to3_get_deps(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
     return results
 
 
-def _2to3_get_dependencies(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
+def _2to3_get_dependencies(conn: AtomicConnection) -> defaultdict[int, list[int]]:
     query = """
             SELECT dependent, independent
             FROM dependencies
@@ -115,7 +115,7 @@ def _2to3_get_dependencies(conn: ConnectionPlus) -> defaultdict[int, list[int]]:
     return results
 
 
-def _2to3_get_layouts(conn: ConnectionPlus) -> dict[int, tuple[str, str, str, str]]:
+def _2to3_get_layouts(conn: AtomicConnection) -> dict[int, tuple[str, str, str, str]]:
     query = """
             SELECT layout_id, parameter, label, unit, inferred_from
             FROM layouts
@@ -130,7 +130,7 @@ def _2to3_get_layouts(conn: ConnectionPlus) -> dict[int, tuple[str, str, str, st
 
 
 def _2to3_get_paramspecs(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     layout_ids: list[int],
     layouts: Mapping[int, tuple[str, str, str, str]],
     dependencies: Mapping[int, Sequence[int]],
@@ -186,7 +186,7 @@ def _2to3_get_paramspecs(
     return paramspecs
 
 
-def upgrade_2_to_3(conn: ConnectionPlus, show_progress_bar: bool = True) -> None:
+def upgrade_2_to_3(conn: AtomicConnection, show_progress_bar: bool = True) -> None:
     """
     Perform the upgrade from version 2 to version 3
 
diff --git a/src/qcodes/dataset/sqlite/db_upgrades/upgrade_3_to_4.py b/src/qcodes/dataset/sqlite/db_upgrades/upgrade_3_to_4.py
index 90d3f13cd58e..7ec70e299e6a 100644
--- a/src/qcodes/dataset/sqlite/db_upgrades/upgrade_3_to_4.py
+++ b/src/qcodes/dataset/sqlite/db_upgrades/upgrade_3_to_4.py
@@ -7,7 +7,11 @@
 from tqdm import tqdm
 
 from qcodes.dataset.descriptions.versioning.v0 import InterDependencies
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic, atomic_transaction
+from qcodes.dataset.sqlite.connection import (
+    AtomicConnection,
+    atomic,
+    atomic_transaction,
+)
 from qcodes.dataset.sqlite.db_upgrades.upgrade_2_to_3 import (
     _2to3_get_dependencies,
     _2to3_get_deps,
@@ -22,7 +26,7 @@
 log = logging.getLogger(__name__)
 
 
-def upgrade_3_to_4(conn: ConnectionPlus, show_progress_bar: bool = True) -> None:
+def upgrade_3_to_4(conn: AtomicConnection, show_progress_bar: bool = True) -> None:
     """
     Perform the upgrade from version 3 to version 4. This really
     repeats the version 3 upgrade as it originally had two bugs in
diff --git a/src/qcodes/dataset/sqlite/db_upgrades/upgrade_5_to_6.py b/src/qcodes/dataset/sqlite/db_upgrades/upgrade_5_to_6.py
index 9153d7b80bf7..abcd50fbacbd 100644
--- a/src/qcodes/dataset/sqlite/db_upgrades/upgrade_5_to_6.py
+++ b/src/qcodes/dataset/sqlite/db_upgrades/upgrade_5_to_6.py
@@ -6,12 +6,16 @@
 from tqdm import tqdm
 
 from qcodes.dataset.descriptions.versioning.v0 import InterDependencies
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic, atomic_transaction
+from qcodes.dataset.sqlite.connection import (
+    AtomicConnection,
+    atomic,
+    atomic_transaction,
+)
 from qcodes.dataset.sqlite.queries import get_run_description, update_run_description
 from qcodes.dataset.sqlite.query_helpers import one
 
 
-def upgrade_5_to_6(conn: ConnectionPlus, show_progress_bar: bool = True) -> None:
+def upgrade_5_to_6(conn: AtomicConnection, show_progress_bar: bool = True) -> None:
     """
     Perform the upgrade from version 5 to version 6.
 
diff --git a/src/qcodes/dataset/sqlite/db_upgrades/version.py b/src/qcodes/dataset/sqlite/db_upgrades/version.py
index b8bb0acafcbc..566a67f5da98 100644
--- a/src/qcodes/dataset/sqlite/db_upgrades/version.py
+++ b/src/qcodes/dataset/sqlite/db_upgrades/version.py
@@ -1,14 +1,14 @@
 from __future__ import annotations
 
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic_transaction
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic_transaction
 from qcodes.dataset.sqlite.query_helpers import one
 
 
-def get_user_version(conn: ConnectionPlus) -> int:
+def get_user_version(conn: AtomicConnection) -> int:
     curr = atomic_transaction(conn, "PRAGMA user_version")
     res = one(curr, 0)
     return res
 
 
-def set_user_version(conn: ConnectionPlus, version: int) -> None:
+def set_user_version(conn: AtomicConnection, version: int) -> None:
     atomic_transaction(conn, f"PRAGMA user_version({version})")
diff --git a/src/qcodes/dataset/sqlite/initial_schema.py b/src/qcodes/dataset/sqlite/initial_schema.py
index b27a9ef43319..7f93b694f1a8 100644
--- a/src/qcodes/dataset/sqlite/initial_schema.py
+++ b/src/qcodes/dataset/sqlite/initial_schema.py
@@ -6,10 +6,10 @@
 
 from __future__ import annotations
 
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic, transaction
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic, transaction
 
 
-def init_db(conn: ConnectionPlus) -> None:
+def init_db(conn: AtomicConnection) -> None:
     with atomic(conn) as atomic_conn:
         transaction(atomic_conn, _experiment_table_schema)
         transaction(atomic_conn, _runs_table_schema)
diff --git a/src/qcodes/dataset/sqlite/queries.py b/src/qcodes/dataset/sqlite/queries.py
index 831e4cd278ea..c992461c875f 100644
--- a/src/qcodes/dataset/sqlite/queries.py
+++ b/src/qcodes/dataset/sqlite/queries.py
@@ -27,7 +27,7 @@
 from qcodes.dataset.descriptions.versioning.converters import new_to_old, old_to_new
 from qcodes.dataset.guids import build_guid_from_components, parse_guid
 from qcodes.dataset.sqlite.connection import (
-    ConnectionPlus,
+    AtomicConnection,
     atomic,
     atomic_transaction,
     transaction,
@@ -89,7 +89,7 @@
 )
 
 
-def is_run_id_in_database(conn: ConnectionPlus, *run_ids: int) -> dict[int, bool]:
+def is_run_id_in_database(conn: AtomicConnection, *run_ids: int) -> dict[int, bool]:
     """
     Look up run_ids and return a dictionary with the answers to the question
     "is this run_id in the database?"
@@ -120,7 +120,7 @@ def is_run_id_in_database(conn: ConnectionPlus, *run_ids: int) -> dict[int, bool
 
 
 def get_parameter_data(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table_name: str,
     columns: Sequence[str] = (),
     start: int | None = None,
@@ -170,7 +170,7 @@ def get_parameter_data(
 
 
 def get_shaped_parameter_data_for_one_paramtree(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table_name: str,
     rundescriber: RunDescriber,
     output_param: str,
@@ -214,7 +214,7 @@ def get_shaped_parameter_data_for_one_paramtree(
 
 
 def get_rundescriber_from_result_table_name(
-    conn: ConnectionPlus, result_table_name: str
+    conn: AtomicConnection, result_table_name: str
 ) -> RunDescriber:
     sql = """
     SELECT run_id FROM runs WHERE result_table_name = ?
@@ -226,7 +226,7 @@ def get_rundescriber_from_result_table_name(
 
 
 def get_parameter_data_for_one_paramtree(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table_name: str,
     rundescriber: RunDescriber,
     output_param: str,
@@ -328,7 +328,7 @@ def _expand_data_to_arrays(
 
 
 def _get_data_for_one_param_tree(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table_name: str,
     interdeps: InterDependencies_,
     output_param: str,
@@ -355,7 +355,9 @@ def _get_data_for_one_param_tree(
     return res, paramspecs, n_rows
 
 
-def get_parameter_db_row(conn: ConnectionPlus, table_name: str, param_name: str) -> int:
+def get_parameter_db_row(
+    conn: AtomicConnection, table_name: str, param_name: str
+) -> int:
     """
     Get the total number of not-null values of a parameter
 
@@ -377,7 +379,7 @@ def get_parameter_db_row(conn: ConnectionPlus, table_name: str, param_name: str)
     return one(c, 0)
 
 
-def get_table_max_id(conn: ConnectionPlus, table_name: str) -> int:
+def get_table_max_id(conn: AtomicConnection, table_name: str) -> int:
     """
     Get the max id of a table
 
@@ -399,7 +401,7 @@ def get_table_max_id(conn: ConnectionPlus, table_name: str) -> int:
 
 
 def _get_offset_limit_for_callback(
-    conn: ConnectionPlus, table_name: str, param_name: str
+    conn: AtomicConnection, table_name: str, param_name: str
 ) -> tuple[np.ndarray, np.ndarray]:
     """
     Since sqlite3 does not allow to keep track of the data loading progress,
@@ -450,7 +452,7 @@ def _get_offset_limit_for_callback(
 
 
 def get_parameter_tree_values(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     result_table_name: str,
     toplevel_param_name: str,
     *other_param_names: str,
@@ -545,7 +547,7 @@ def get_parameter_tree_values(
 
 
 def get_runid_from_expid_and_counter(
-    conn: ConnectionPlus, exp_id: int, counter: int
+    conn: AtomicConnection, exp_id: int, counter: int
 ) -> int:
     """
     Get the run_id of a run in the specified experiment with the specified
@@ -569,7 +571,7 @@ def get_runid_from_expid_and_counter(
 
 
 def get_guid_from_expid_and_counter(
-    conn: ConnectionPlus, exp_id: int, counter: int
+    conn: AtomicConnection, exp_id: int, counter: int
 ) -> str:
     """
     Get the guid of a run in the specified experiment with the specified
@@ -592,7 +594,7 @@ def get_guid_from_expid_and_counter(
     return run_id
 
 
-def get_runid_from_guid(conn: ConnectionPlus, guid: str) -> int | None:
+def get_runid_from_guid(conn: AtomicConnection, guid: str) -> int | None:
     """
     Get the run_id of a run based on the guid
 
@@ -632,7 +634,7 @@ def get_runid_from_guid(conn: ConnectionPlus, guid: str) -> int | None:
 
 
 def _query_guids_from_run_spec(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     captured_run_id: int | None = None,
     captured_counter: int | None = None,
     experiment_name: str | None = None,
@@ -702,7 +704,7 @@ def _query_guids_from_run_spec(
 
 
 def _get_layout_id(
-    conn: ConnectionPlus, parameter: ParamSpec | str, run_id: int
+    conn: AtomicConnection, parameter: ParamSpec | str, run_id: int
 ) -> int:
     """
     Get the layout id of a parameter in a given run
@@ -736,7 +738,7 @@ def _get_layout_id(
     return res
 
 
-def _get_dependents(conn: ConnectionPlus, run_id: int) -> list[int]:
+def _get_dependents(conn: AtomicConnection, run_id: int) -> list[int]:
     """
     Get dependent layout_ids for a certain run_id, i.e. the layout_ids of all
     the dependent variables
@@ -750,7 +752,7 @@ def _get_dependents(conn: ConnectionPlus, run_id: int) -> list[int]:
     return res
 
 
-def _get_dependencies(conn: ConnectionPlus, layout_id: int) -> list[tuple[int, int]]:
+def _get_dependencies(conn: AtomicConnection, layout_id: int) -> list[tuple[int, int]]:
     """
     Get the dependencies of a certain dependent variable (indexed by its
     layout_id)
@@ -771,7 +773,7 @@ def _get_dependencies(conn: ConnectionPlus, layout_id: int) -> list[tuple[int, i
 
 
 def new_experiment(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     name: str,
     sample_name: str,
     format_string: str | None = "{}-{}-{}",
@@ -818,7 +820,7 @@ def new_experiment(
 # TODO(WilliamHPNielsen): we should remove the redundant
 # is_completed
 def mark_run_complete(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     run_id: int,
     timestamp: float | None = None,
     override: bool = False,
@@ -853,7 +855,7 @@ def mark_run_complete(
     atomic_transaction(conn, query, timestamp, True, run_id)
 
 
-def completed(conn: ConnectionPlus, run_id: int) -> bool:
+def completed(conn: AtomicConnection, run_id: int) -> bool:
     """Check if the run is complete
 
     Args:
@@ -865,7 +867,7 @@ def completed(conn: ConnectionPlus, run_id: int) -> bool:
 
 
 def get_completed_timestamp_from_run_id(
-    conn: ConnectionPlus, run_id: int
+    conn: AtomicConnection, run_id: int
 ) -> float | None:
     """
     Retrieve the timestamp when the given measurement run was completed
@@ -889,7 +891,7 @@ def get_completed_timestamp_from_run_id(
     return ts
 
 
-def get_guid_from_run_id(conn: ConnectionPlus, run_id: int) -> str | None:
+def get_guid_from_run_id(conn: AtomicConnection, run_id: int) -> str | None:
     """
     Get the guid of the given run. Returns None if the run is not found
 
@@ -910,7 +912,7 @@ def get_guid_from_run_id(conn: ConnectionPlus, run_id: int) -> str | None:
 
 
 def get_guids_from_multiple_run_ids(
-    conn: ConnectionPlus, run_ids: Iterable[int]
+    conn: AtomicConnection, run_ids: Iterable[int]
 ) -> list[str]:
     """
     Retrieve guids of runs in the connected database specified by their run ids.
@@ -937,7 +939,7 @@ def get_guids_from_multiple_run_ids(
     return guids
 
 
-def finish_experiment(conn: ConnectionPlus, exp_id: int) -> None:
+def finish_experiment(conn: AtomicConnection, exp_id: int) -> None:
     """Finish experiment
 
     Args:
@@ -951,7 +953,7 @@ def finish_experiment(conn: ConnectionPlus, exp_id: int) -> None:
     atomic_transaction(conn, query, time.time(), exp_id)
 
 
-def get_run_counter(conn: ConnectionPlus, exp_id: int) -> int:
+def get_run_counter(conn: AtomicConnection, exp_id: int) -> int:
     """Get the experiment run counter
 
     Args:
@@ -971,7 +973,7 @@ def get_run_counter(conn: ConnectionPlus, exp_id: int) -> int:
     return counter
 
 
-def get_experiments(conn: ConnectionPlus) -> list[int]:
+def get_experiments(conn: AtomicConnection) -> list[int]:
     """
     Get a list of experiments
 
@@ -988,7 +990,7 @@ def get_experiments(conn: ConnectionPlus) -> list[int]:
     return [exp_id for (exp_id,) in c.fetchall()]
 
 
-def get_matching_exp_ids(conn: ConnectionPlus, **match_conditions: Any) -> list[int]:
+def get_matching_exp_ids(conn: AtomicConnection, **match_conditions: Any) -> list[int]:
     """
     Get exp_ids for experiments matching the match_conditions
 
@@ -1036,7 +1038,9 @@ def get_matching_exp_ids(conn: ConnectionPlus, **match_conditions: Any) -> list[
     return [exp_id for (exp_id,) in cursor.fetchall()]
 
 
-def get_exp_ids_from_run_ids(conn: ConnectionPlus, run_ids: Sequence[int]) -> list[int]:
+def get_exp_ids_from_run_ids(
+    conn: AtomicConnection, run_ids: Sequence[int]
+) -> list[int]:
     """
     Get the corresponding exp_id for a sequence of run_ids
 
@@ -1061,7 +1065,7 @@ def get_exp_ids_from_run_ids(conn: ConnectionPlus, run_ids: Sequence[int]) -> li
     return [exp_id for row in rows for exp_id in row]
 
 
-def get_last_experiment(conn: ConnectionPlus) -> int | None:
+def get_last_experiment(conn: AtomicConnection) -> int | None:
     """
     Return last started experiment id
 
@@ -1072,7 +1076,7 @@ def get_last_experiment(conn: ConnectionPlus) -> int | None:
     return c.fetchall()[0][0]
 
 
-def get_runs(conn: ConnectionPlus, exp_id: int | None = None) -> list[int]:
+def get_runs(conn: AtomicConnection, exp_id: int | None = None) -> list[int]:
     """Get a list of runs.
 
     Args:
@@ -1098,7 +1102,7 @@ def get_runs(conn: ConnectionPlus, exp_id: int | None = None) -> list[int]:
     return [run_id for (run_id,) in c.fetchall()]
 
 
-def get_last_run(conn: ConnectionPlus, exp_id: int | None = None) -> int | None:
+def get_last_run(conn: AtomicConnection, exp_id: int | None = None) -> int | None:
     """
     Get run_id of the last run in experiment with exp_id
 
@@ -1128,7 +1132,7 @@ def get_last_run(conn: ConnectionPlus, exp_id: int | None = None) -> int | None:
     return one(c, "run_id")
 
 
-def run_exists(conn: ConnectionPlus, run_id: int) -> bool:
+def run_exists(conn: AtomicConnection, run_id: int) -> bool:
     # the following query always returns a single tuple with an integer
     # value of `1` or `0` for existing and non-existing run_id in the database
     query = """
@@ -1160,7 +1164,7 @@ def format_table_name(fmt_str: str, name: str, exp_id: int, run_counter: int) ->
 
 
 def _insert_run(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     exp_id: int,
     name: str,
     guid: str,
@@ -1324,7 +1328,7 @@ def _insert_run(
 
 
 def _update_experiment_run_counter(
-    conn: ConnectionPlus, exp_id: int, run_counter: int
+    conn: AtomicConnection, exp_id: int, run_counter: int
 ) -> None:
     query = """
     UPDATE experiments
@@ -1334,7 +1338,7 @@ def _update_experiment_run_counter(
     atomic_transaction(conn, query, run_counter, exp_id)
 
 
-def _get_parameters(conn: ConnectionPlus, run_id: int) -> list[ParamSpec]:
+def _get_parameters(conn: AtomicConnection, run_id: int) -> list[ParamSpec]:
     """
     Get the list of param specs for run
 
@@ -1358,7 +1362,7 @@ def _get_parameters(conn: ConnectionPlus, run_id: int) -> list[ParamSpec]:
     ]
 
 
-def _get_paramspec(conn: ConnectionPlus, run_id: int, param_name: str) -> ParamSpec:
+def _get_paramspec(conn: AtomicConnection, run_id: int, param_name: str) -> ParamSpec:
     """
     Get the ParamSpec object for the given parameter name
     in the given run
@@ -1427,7 +1431,9 @@ def _get_paramspec(conn: ConnectionPlus, run_id: int, param_name: str) -> ParamS
     return parspec
 
 
-def update_run_description(conn: ConnectionPlus, run_id: int, description: str) -> None:
+def update_run_description(
+    conn: AtomicConnection, run_id: int, description: str
+) -> None:
     """
     Update the run_description field for the given run_id. The description
     string must be a valid JSON string representation of a RunDescriber object
@@ -1444,7 +1450,7 @@ def update_run_description(conn: ConnectionPlus, run_id: int, description: str)
 
 
 def _update_run_description(
-    conn: ConnectionPlus, run_id: int, description: str
+    conn: AtomicConnection, run_id: int, description: str
 ) -> None:
     """
     Update the run_description field for the given run_id. The description
@@ -1459,7 +1465,7 @@ def _update_run_description(
         atomic_conn.cursor().execute(sql, (description, run_id))
 
 
-def update_parent_datasets(conn: ConnectionPlus, run_id: int, links_str: str) -> None:
+def update_parent_datasets(conn: AtomicConnection, run_id: int, links_str: str) -> None:
     """
     Update (i.e. overwrite) the parent_datasets field for the given run_id
     """
@@ -1476,7 +1482,7 @@ def update_parent_datasets(conn: ConnectionPlus, run_id: int, links_str: str) ->
 
 
 def set_run_timestamp(
-    conn: ConnectionPlus, run_id: int, timestamp: float | None = None
+    conn: AtomicConnection, run_id: int, timestamp: float | None = None
 ) -> None:
     """
     Set the run_timestamp for the run with the given run_id. If the
@@ -1518,7 +1524,7 @@ def set_run_timestamp(
 
 def add_parameter(
     *parameter: ParamSpec,
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     run_id: int,
     insert_into_results_table: bool,
 ) -> None:
@@ -1567,7 +1573,7 @@ def add_parameter(
 
 
 def _add_parameters_to_layout_and_deps(
-    conn: ConnectionPlus, run_id: int, *parameter: ParamSpec
+    conn: AtomicConnection, run_id: int, *parameter: ParamSpec
 ) -> sqlite3.Cursor:
     layout_args: list[int | str] = []
     for p in parameter:
@@ -1619,7 +1625,7 @@ def _validate_table_name(table_name: str) -> bool:
 
 
 def _create_run_table(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     formatted_name: str,
     parameters: Sequence[ParamSpecBase] | None = None,
     values: VALUES | None = None,
@@ -1668,7 +1674,7 @@ def _create_run_table(
 
 
 def create_run(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     exp_id: int,
     name: str,
     guid: str,
@@ -1763,7 +1769,7 @@ def create_run(
     return run_counter, run_id, formatted_name
 
 
-def get_run_description(conn: ConnectionPlus, run_id: int) -> str:
+def get_run_description(conn: AtomicConnection, run_id: int) -> str:
     """
     Return the (JSON string) run description of the specified run
     """
@@ -1772,7 +1778,7 @@ def get_run_description(conn: ConnectionPlus, run_id: int) -> str:
     return rds
 
 
-def get_parent_dataset_links(conn: ConnectionPlus, run_id: int) -> str:
+def get_parent_dataset_links(conn: AtomicConnection, run_id: int) -> str:
     """
     Return the (JSON string) of the parent-child dataset links for the
     specified run
@@ -1802,7 +1808,7 @@ def get_parent_dataset_links(conn: ConnectionPlus, run_id: int) -> str:
 
 
 def get_data_by_tag_and_table_name(
-    conn: ConnectionPlus, tag: str, table_name: str
+    conn: AtomicConnection, tag: str, table_name: str
 ) -> VALUE | None:
     """
     Get data from the "tag" column for the row in "runs" table where
@@ -1825,7 +1831,7 @@ def get_data_by_tag_and_table_name(
     return data
 
 
-def get_metadata_from_run_id(conn: ConnectionPlus, run_id: int) -> dict[str, Any]:
+def get_metadata_from_run_id(conn: AtomicConnection, run_id: int) -> dict[str, Any]:
     """
     Get all metadata associated with the specified run
     """
@@ -1879,7 +1885,7 @@ def validate_dynamic_column_data(data: Mapping[str, Any]) -> None:
 
 
 def insert_data_in_dynamic_columns(
-    conn: ConnectionPlus, row_id: int, table_name: str, data: Mapping[str, Any]
+    conn: AtomicConnection, row_id: int, table_name: str, data: Mapping[str, Any]
 ) -> None:
     """
     Insert new data column and add values. Note that None is not a valid
@@ -1900,7 +1906,7 @@ def insert_data_in_dynamic_columns(
 
 
 def update_columns(
-    conn: ConnectionPlus, row_id: int, table_name: str, data: Mapping[str, Any]
+    conn: AtomicConnection, row_id: int, table_name: str, data: Mapping[str, Any]
 ) -> None:
     """
     Updates data in columns matching the given keys (they must exist already)
@@ -1917,7 +1923,10 @@ def update_columns(
 
 
 def add_data_to_dynamic_columns(
-    conn: ConnectionPlus, row_id: int, data: Mapping[str, Any], table_name: str = "runs"
+    conn: AtomicConnection,
+    row_id: int,
+    data: Mapping[str, Any],
+    table_name: str = "runs",
 ) -> None:
     """
     Add columns from keys and insert values.
@@ -1945,13 +1954,13 @@ def add_data_to_dynamic_columns(
             raise e
 
 
-def get_experiment_name_from_experiment_id(conn: ConnectionPlus, exp_id: int) -> str:
+def get_experiment_name_from_experiment_id(conn: AtomicConnection, exp_id: int) -> str:
     exp_name = select_one_where(conn, "experiments", "name", "exp_id", exp_id)
     assert isinstance(exp_name, str)
     return exp_name
 
 
-def get_sample_name_from_experiment_id(conn: ConnectionPlus, exp_id: int) -> str:
+def get_sample_name_from_experiment_id(conn: AtomicConnection, exp_id: int) -> str:
     sample_name = select_one_where(conn, "experiments", "sample_name", "exp_id", exp_id)
     assert isinstance(sample_name, (str, type(None)))
     # there may be a few cases for very old db where None is returned as a sample name
@@ -1960,7 +1969,7 @@ def get_sample_name_from_experiment_id(conn: ConnectionPlus, exp_id: int) -> str
     return cast("str", sample_name)
 
 
-def get_run_timestamp_from_run_id(conn: ConnectionPlus, run_id: int) -> float | None:
+def get_run_timestamp_from_run_id(conn: AtomicConnection, run_id: int) -> float | None:
     time_stamp = select_one_where(conn, "runs", "run_timestamp", "run_id", run_id)
     # sometimes it happens that the timestamp is saved as an integer in the database
     if isinstance(time_stamp, int):
@@ -1969,7 +1978,7 @@ def get_run_timestamp_from_run_id(conn: ConnectionPlus, run_id: int) -> float |
     return time_stamp
 
 
-def update_GUIDs(conn: ConnectionPlus) -> None:
+def update_GUIDs(conn: AtomicConnection) -> None:
     """
     Update all GUIDs in this database where either the location code or the
     work_station code is zero to use the location and work_station code from
@@ -2023,7 +2032,7 @@ def _workstation_only_zero(run_id: int, *args: Any) -> None:
         )
 
     def _both_zero(
-        run_id: int, conn: ConnectionPlus, guid_comps: dict[str, Any]
+        run_id: int, conn: AtomicConnection, guid_comps: dict[str, Any]
     ) -> None:
         guid_str = build_guid_from_components(guid_comps)
         with atomic(conn) as atomic_conn:
@@ -2037,7 +2046,7 @@ def _both_zero(
         log.info(f"Succesfully updated run number {run_id}.")
 
     actions: dict[
-        tuple[bool, bool], Callable[[int, ConnectionPlus, dict[str, Any]], None]
+        tuple[bool, bool], Callable[[int, AtomicConnection, dict[str, Any]], None]
     ]
     actions = {
         (True, True): _both_zero,
@@ -2060,7 +2069,7 @@ def _both_zero(
         actions[(old_loc == 0, old_ws == 0)](run_id, conn, guid_comps)
 
 
-def remove_trigger(conn: ConnectionPlus, trigger_id: str) -> None:
+def remove_trigger(conn: AtomicConnection, trigger_id: str) -> None:
     """
     Removes a trigger with a given id if it exists.
 
@@ -2075,7 +2084,7 @@ def remove_trigger(conn: ConnectionPlus, trigger_id: str) -> None:
 
 
 def load_new_data_for_rundescriber(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table_name: str,
     rundescriber: RunDescriber,
     read_status: Mapping[str, int],
@@ -2125,7 +2134,7 @@ class ExperimentAttributeDict(TypedDict):
 
 
 def get_experiment_attributes_by_exp_id(
-    conn: ConnectionPlus, exp_id: int
+    conn: AtomicConnection, exp_id: int
 ) -> ExperimentAttributeDict:
     """
     Return a dict of all attributes describing an experiment from the exp_id.
@@ -2163,8 +2172,8 @@ def get_experiment_attributes_by_exp_id(
 
 
 def _populate_results_table(
-    source_conn: ConnectionPlus,
-    target_conn: ConnectionPlus,
+    source_conn: AtomicConnection,
+    target_conn: AtomicConnection,
     source_table_name: str,
     target_table_name: str,
 ) -> None:
@@ -2194,7 +2203,7 @@ def _populate_results_table(
 
 
 def _rewrite_timestamps(
-    target_conn: ConnectionPlus,
+    target_conn: AtomicConnection,
     target_run_id: int,
     correct_run_timestamp: float | None,
     correct_completed_timestamp: float | None,
@@ -2235,7 +2244,7 @@ class RawRunAttributesDict(TypedDict):
 
 
 def get_raw_run_attributes(
-    conn: ConnectionPlus, guid: str
+    conn: AtomicConnection, guid: str
 ) -> RawRunAttributesDict | None:
     run_id = get_runid_from_guid(conn, guid)
 
@@ -2285,13 +2294,13 @@ def raw_time_to_str_time(
         return time.strftime(fmt, time.localtime(raw_timestamp))
 
 
-def _check_if_table_found(conn: ConnectionPlus, table_name: str) -> bool:
+def _check_if_table_found(conn: AtomicConnection, table_name: str) -> bool:
     query = "SELECT name FROM sqlite_master WHERE type='table' AND name=?"
     cursor = conn.cursor()
     return not many_many(cursor.execute(query, (table_name,)), "name") == []
 
 
-def _get_result_table_name_by_guid(conn: ConnectionPlus, guid: str) -> str:
+def _get_result_table_name_by_guid(conn: AtomicConnection, guid: str) -> str:
     sql = "SELECT result_table_name FROM runs WHERE guid=?"
     formatted_name = one(transaction(conn, sql, guid), "result_table_name")
     return formatted_name
diff --git a/src/qcodes/dataset/sqlite/query_helpers.py b/src/qcodes/dataset/sqlite/query_helpers.py
index 60a122529b10..afeb5c15c561 100644
--- a/src/qcodes/dataset/sqlite/query_helpers.py
+++ b/src/qcodes/dataset/sqlite/query_helpers.py
@@ -14,7 +14,7 @@
 from packaging import version
 
 from qcodes.dataset.sqlite.connection import (
-    ConnectionPlus,
+    AtomicConnection,
     atomic,
     atomic_transaction,
     transaction,
@@ -140,7 +140,11 @@ def many_many(curr: sqlite3.Cursor, *columns: str) -> list[tuple[Any, ...]]:
 
 
 def select_one_where(
-    conn: ConnectionPlus, table: str, column: str, where_column: str, where_value: VALUE
+    conn: AtomicConnection,
+    table: str,
+    column: str,
+    where_column: str,
+    where_value: VALUE,
 ) -> VALUE:
     """
     Select a value from a given column given a match of a value in a
@@ -176,7 +180,7 @@ def select_one_where(
 
 
 def select_many_where(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table: str,
     *columns: str,
     where_column: str,
@@ -208,7 +212,7 @@ def _massage_dict(metadata: Mapping[str, Any]) -> tuple[str, list[Any]]:
 
 
 def update_where(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     table: str,
     where_column: str,
     where_value: Any,
@@ -227,7 +231,7 @@ def update_where(
 
 
 def insert_values(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     formatted_name: str,
     columns: list[str],
     values: VALUES,
@@ -253,7 +257,7 @@ def insert_values(
 
 
 def insert_many_values(
-    conn: ConnectionPlus,
+    conn: AtomicConnection,
     formatted_name: str,
     columns: Sequence[str],
     values: Sequence[VALUES],
@@ -331,7 +335,7 @@ def insert_many_values(
     return return_value
 
 
-def length(conn: ConnectionPlus, formatted_name: str) -> int:
+def length(conn: AtomicConnection, formatted_name: str) -> int:
     """
     Return the length of the table
 
@@ -358,7 +362,7 @@ def length(conn: ConnectionPlus, formatted_name: str) -> int:
 
 
 def insert_column(
-    conn: ConnectionPlus, table: str, name: str, paramtype: str | None = None
+    conn: AtomicConnection, table: str, name: str, paramtype: str | None = None
 ) -> None:
     """Insert new column to a table
 
@@ -388,7 +392,7 @@ def insert_column(
             transaction(atomic_conn, f'ALTER TABLE "{table}" ADD COLUMN "{name}"')
 
 
-def is_column_in_table(conn: ConnectionPlus, table: str, column: str) -> bool:
+def is_column_in_table(conn: AtomicConnection, table: str, column: str) -> bool:
     """
     A look-before-you-leap function to look up if a table has a certain column.
 
diff --git a/tests/dataset/test_database_creation_and_upgrading.py b/tests/dataset/test_database_creation_and_upgrading.py
index e35bf8e7fdef..8679a71867a6 100644
--- a/tests/dataset/test_database_creation_and_upgrading.py
+++ b/tests/dataset/test_database_creation_and_upgrading.py
@@ -11,7 +11,6 @@
 import qcodes.dataset.descriptions.versioning.serialization as serial
 import tests.dataset
 from qcodes.dataset import (
-    ConnectionPlus,
     connect,
     initialise_database,
     initialise_or_create_database_at,
@@ -26,7 +25,7 @@
 from qcodes.dataset.descriptions.param_spec import ParamSpecBase
 from qcodes.dataset.descriptions.versioning.v0 import InterDependencies
 from qcodes.dataset.guids import parse_guid
-from qcodes.dataset.sqlite.connection import atomic_transaction
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic_transaction
 from qcodes.dataset.sqlite.database import get_db_version_and_newest_available_version
 from qcodes.dataset.sqlite.db_upgrades import (
     _latest_available_version,
@@ -703,7 +702,7 @@ def test_perform_actual_upgrade_6_to_7() -> None:
     skip_if_no_fixtures(dbname_old)
 
     with temporarily_copied_DB(dbname_old, debug=False, version=6) as conn:
-        assert isinstance(conn, ConnectionPlus)
+        assert isinstance(conn, AtomicConnection)
         perform_db_upgrade_6_to_7(conn)
         assert get_user_version(conn) == 7
 
@@ -762,7 +761,7 @@ def test_perform_actual_upgrade_6_to_newest_add_new_data() -> None:
     skip_if_no_fixtures(dbname_old)
 
     with temporarily_copied_DB(dbname_old, debug=False, version=6) as conn:
-        assert isinstance(conn, ConnectionPlus)
+        assert isinstance(conn, AtomicConnection)
         perform_db_upgrade(conn)
         assert get_user_version(conn) >= 7
         no_of_runs_query = "SELECT max(run_id) FROM runs"
diff --git a/tests/dataset/test_dataset_in_memory.py b/tests/dataset/test_dataset_in_memory.py
index f32519495d20..a6741d955ce7 100644
--- a/tests/dataset/test_dataset_in_memory.py
+++ b/tests/dataset/test_dataset_in_memory.py
@@ -1,7 +1,6 @@
 import contextlib
 import os
 import shutil
-import sqlite3
 from pathlib import Path
 
 import hypothesis.strategies as hst
@@ -15,7 +14,7 @@
 from qcodes.dataset import load_by_id, load_by_run_spec
 from qcodes.dataset.data_set_in_memory import DataSetInMem, load_from_file
 from qcodes.dataset.data_set_protocol import DataSetType
-from qcodes.dataset.sqlite.connection import ConnectionPlus, atomic_transaction
+from qcodes.dataset.sqlite.connection import AtomicConnection, atomic_transaction
 from qcodes.station import Station
 
 
@@ -362,7 +361,7 @@ def test_dataset_in_memory_does_not_create_runs_table(
     ds = datasaver.dataset
     dbfile = datasaver.dataset._path_to_db
 
-    conn = ConnectionPlus(sqlite3.connect(dbfile))
+    conn = AtomicConnection(dbfile)
 
     tables_query = 'SELECT * FROM sqlite_master WHERE TYPE = "table"'
     tables = list(atomic_transaction(conn, tables_query).fetchall())
diff --git a/tests/dataset/test_guid_helpers.py b/tests/dataset/test_guid_helpers.py
index 23b727151c80..8b775a034ad5 100644
--- a/tests/dataset/test_guid_helpers.py
+++ b/tests/dataset/test_guid_helpers.py
@@ -17,7 +17,7 @@
 if TYPE_CHECKING:
     from pathlib import Path
 
-    from qcodes.dataset.sqlite.connection import ConnectionPlus
+    from qcodes.dataset.sqlite.connection import AtomicConnection
 
 
 def test_guids_from_dir(tmp_path: "Path") -> None:
@@ -92,7 +92,7 @@ def test_many_guids_from_list_str() -> None:
 
 
 def test_get_guids_from_multiple_run_ids(tmp_path: "Path") -> None:
-    def generate_local_exp(dbpath: "Path") -> tuple[list[str], "ConnectionPlus"]:
+    def generate_local_exp(dbpath: "Path") -> tuple[list[str], "AtomicConnection"]:
         with initialised_database_at(str(dbpath)):
             guids = []
             exp = load_or_create_experiment(experiment_name="test_guid")
diff --git a/tests/dataset/test_sqlite_connection.py b/tests/dataset/test_sqlite_connection.py
index 864abc3450fe..94eacb61fd72 100644
--- a/tests/dataset/test_sqlite_connection.py
+++ b/tests/dataset/test_sqlite_connection.py
@@ -4,10 +4,11 @@
 import pytest
 
 from qcodes.dataset.sqlite.connection import (
-    ConnectionPlus,
+    AtomicConnection,
+    ConnectionPlus,  # pyright: ignore[reportDeprecated]
     atomic,
     atomic_transaction,
-    make_connection_plus_from,
+    make_connection_plus_from,  # pyright: ignore[reportDeprecated]
 )
 from qcodes.dataset.sqlite.database import connect
 from tests.common import error_caused_by
@@ -20,8 +21,8 @@ def sqlite_conn_in_transaction(conn: sqlite3.Connection):
     return True
 
 
-def conn_plus_in_transaction(conn: ConnectionPlus):
-    assert isinstance(conn, ConnectionPlus)
+def conn_plus_in_transaction(conn: AtomicConnection):
+    assert isinstance(conn, AtomicConnection | ConnectionPlus)  # pyright: ignore[reportDeprecated]
     assert True is conn.atomic_in_progress
     assert None is conn.isolation_level
     assert True is conn.in_transaction
@@ -35,8 +36,8 @@ def sqlite_conn_is_idle(conn: sqlite3.Connection, isolation=None):
     return True
 
 
-def conn_plus_is_idle(conn: ConnectionPlus, isolation=None):
-    assert isinstance(conn, ConnectionPlus)
+def conn_plus_is_idle(conn: ConnectionPlus | AtomicConnection, isolation=None):  # pyright: ignore[reportDeprecated]
+    assert isinstance(conn, ConnectionPlus | AtomicConnection)  # pyright: ignore[reportDeprecated]
     assert False is conn.atomic_in_progress
     assert isolation == conn.isolation_level
     assert False is conn.in_transaction
@@ -45,10 +46,10 @@ def conn_plus_is_idle(conn: ConnectionPlus, isolation=None):
 
 def test_connection_plus() -> None:
     sqlite_conn = sqlite3.connect(":memory:")
-    conn_plus = ConnectionPlus(sqlite_conn)
+    conn_plus = ConnectionPlus(sqlite_conn)  # pyright: ignore[reportDeprecated]
 
     assert conn_plus.path_to_dbfile == ""
-    assert isinstance(conn_plus, ConnectionPlus)
+    assert isinstance(conn_plus, ConnectionPlus)  # pyright: ignore[reportDeprecated]
     assert isinstance(conn_plus, sqlite3.Connection)
     assert False is conn_plus.atomic_in_progress
 
@@ -57,41 +58,72 @@ def test_connection_plus() -> None:
         "`ConnectionPlus` object which is not allowed."
     )
     with pytest.raises(ValueError, match=match_str):
-        ConnectionPlus(conn_plus)
+        ConnectionPlus(conn_plus)  # pyright: ignore[reportDeprecated]
+
+
+def test_atomic_connection() -> None:
+    sqlite_conn = AtomicConnection(":memory:")
+
+    assert sqlite_conn.path_to_dbfile == ""
+    assert isinstance(sqlite_conn, AtomicConnection)
+    assert isinstance(sqlite_conn, sqlite3.Connection)
+    assert False is sqlite_conn.atomic_in_progress
 
 
 def test_make_connection_plus_from_sqlite3_connection() -> None:
     conn = sqlite3.connect(":memory:")
-    conn_plus = make_connection_plus_from(conn)
+    conn_plus = make_connection_plus_from(conn)  # pyright: ignore[reportDeprecated]
 
     assert conn_plus.path_to_dbfile == ""
-    assert isinstance(conn_plus, ConnectionPlus)
+    assert isinstance(conn_plus, ConnectionPlus)  # pyright: ignore[reportDeprecated]
     assert False is conn_plus.atomic_in_progress
     assert conn_plus is not conn
 
 
 def test_make_connection_plus_from_connecton_plus() -> None:
-    conn = ConnectionPlus(sqlite3.connect(":memory:"))
-    conn_plus = make_connection_plus_from(conn)
+    conn = ConnectionPlus(sqlite3.connect(":memory:"))  # pyright: ignore[reportDeprecated]
+    conn_plus = make_connection_plus_from(conn)  # pyright: ignore[reportDeprecated]
 
     assert conn_plus.path_to_dbfile == ""
-    assert isinstance(conn_plus, ConnectionPlus)
+    assert isinstance(conn_plus, ConnectionPlus)  # pyright: ignore[reportDeprecated]
     assert conn.atomic_in_progress is conn_plus.atomic_in_progress
     assert conn_plus is conn
 
 
-def test_atomic() -> None:
+def test_atomic_connection_plus() -> None:
     sqlite_conn = sqlite3.connect(":memory:")
 
     match_str = re.escape(
-        "atomic context manager only accepts ConnectionPlus "
+        "atomic context manager only accepts AtomicConnection or ConnectionPlus "
         "database connection objects."
     )
     with pytest.raises(ValueError, match=match_str):
         with atomic(sqlite_conn):  # type: ignore[arg-type]
             pass
 
-    conn_plus = ConnectionPlus(sqlite_conn)
+    conn_plus = ConnectionPlus(sqlite_conn)  # pyright: ignore[reportDeprecated]
+    assert False is conn_plus.atomic_in_progress
+
+    atomic_in_progress = conn_plus.atomic_in_progress
+    isolation_level = conn_plus.isolation_level
+
+    assert False is conn_plus.in_transaction
+
+    with atomic(conn_plus) as atomic_conn:
+        assert conn_plus_in_transaction(atomic_conn)
+        assert conn_plus_in_transaction(conn_plus)
+
+    assert isolation_level == conn_plus.isolation_level
+    assert False is conn_plus.in_transaction
+    assert atomic_in_progress is conn_plus.atomic_in_progress
+
+    assert isolation_level == conn_plus.isolation_level
+    assert False is atomic_conn.in_transaction
+    assert atomic_in_progress is atomic_conn.atomic_in_progress
+
+
+def test_atomic() -> None:
+    conn_plus = AtomicConnection(":memory:")
     assert False is conn_plus.atomic_in_progress
 
     atomic_in_progress = conn_plus.atomic_in_progress
@@ -113,8 +145,7 @@ def test_atomic() -> None:
 
 
 def test_atomic_with_exception() -> None:
-    sqlite_conn = sqlite3.connect(":memory:")
-    conn_plus = ConnectionPlus(sqlite_conn)
+    sqlite_conn = AtomicConnection(":memory:")
 
     sqlite_conn.execute("PRAGMA user_version(25)")
     sqlite_conn.commit()
@@ -124,7 +155,7 @@ def test_atomic_with_exception() -> None:
     with pytest.raises(
         RuntimeError, match="Rolling back due to unhandled exception"
     ) as e:
-        with atomic(conn_plus) as atomic_conn:
+        with atomic(sqlite_conn) as atomic_conn:
             atomic_conn.execute("PRAGMA user_version(42)")
             raise Exception("intended exception")
     assert error_caused_by(e, "intended exception")
@@ -133,7 +164,7 @@ def test_atomic_with_exception() -> None:
 
 
 def test_atomic_on_outmost_connection_that_is_in_transaction() -> None:
-    conn = ConnectionPlus(sqlite3.connect(":memory:"))
+    conn = AtomicConnection(":memory:")
 
     conn.execute("BEGIN")
     assert True is conn.in_transaction
@@ -150,32 +181,31 @@ def test_atomic_on_outmost_connection_that_is_in_transaction() -> None:
 
 @pytest.mark.parametrize("in_transaction", (True, False))
 def test_atomic_on_connection_plus_that_is_in_progress(in_transaction) -> None:
-    sqlite_conn = sqlite3.connect(":memory:")
-    conn_plus = ConnectionPlus(sqlite_conn)
+    sqlite_conn = AtomicConnection(":memory:")
 
     # explicitly set to True for testing purposes
-    conn_plus.atomic_in_progress = True
+    sqlite_conn.atomic_in_progress = True
 
     # implement parametrizing over connection's `in_transaction` attribute
     if in_transaction:
-        conn_plus.cursor().execute("BEGIN")
-    assert in_transaction is conn_plus.in_transaction
+        sqlite_conn.cursor().execute("BEGIN")
+    assert in_transaction is sqlite_conn.in_transaction
 
-    isolation_level = conn_plus.isolation_level
-    in_transaction = conn_plus.in_transaction
+    isolation_level = sqlite_conn.isolation_level
+    in_transaction = sqlite_conn.in_transaction
 
-    with atomic(conn_plus) as atomic_conn:
-        assert True is conn_plus.atomic_in_progress
-        assert isolation_level == conn_plus.isolation_level
-        assert in_transaction is conn_plus.in_transaction
+    with atomic(sqlite_conn) as atomic_conn:
+        assert True is sqlite_conn.atomic_in_progress
+        assert isolation_level == sqlite_conn.isolation_level
+        assert in_transaction is sqlite_conn.in_transaction
 
         assert True is atomic_conn.atomic_in_progress
         assert isolation_level == atomic_conn.isolation_level
         assert in_transaction is atomic_conn.in_transaction
 
-    assert True is conn_plus.atomic_in_progress
-    assert isolation_level == conn_plus.isolation_level
-    assert in_transaction is conn_plus.in_transaction
+    assert True is sqlite_conn.atomic_in_progress
+    assert isolation_level == sqlite_conn.isolation_level
+    assert in_transaction is sqlite_conn.in_transaction
 
     assert True is atomic_conn.atomic_in_progress
     assert isolation_level == atomic_conn.isolation_level
@@ -183,39 +213,38 @@ def test_atomic_on_connection_plus_that_is_in_progress(in_transaction) -> None:
 
 
 def test_two_nested_atomics() -> None:
-    sqlite_conn = sqlite3.connect(":memory:")
-    conn_plus = ConnectionPlus(sqlite_conn)
+    sqlite_conn = AtomicConnection(":memory:")
 
-    atomic_in_progress = conn_plus.atomic_in_progress
-    isolation_level = conn_plus.isolation_level
+    atomic_in_progress = sqlite_conn.atomic_in_progress
+    isolation_level = sqlite_conn.isolation_level
 
-    assert False is conn_plus.in_transaction
+    assert False is sqlite_conn.in_transaction
 
-    with atomic(conn_plus) as atomic_conn_1:
-        assert conn_plus_in_transaction(conn_plus)
+    with atomic(sqlite_conn) as atomic_conn_1:
+        assert conn_plus_in_transaction(sqlite_conn)
         assert conn_plus_in_transaction(atomic_conn_1)
 
         with atomic(atomic_conn_1) as atomic_conn_2:
-            assert conn_plus_in_transaction(conn_plus)
+            assert conn_plus_in_transaction(sqlite_conn)
             assert conn_plus_in_transaction(atomic_conn_1)
             assert conn_plus_in_transaction(atomic_conn_2)
 
-        assert conn_plus_in_transaction(conn_plus)
+        assert conn_plus_in_transaction(sqlite_conn)
         assert conn_plus_in_transaction(atomic_conn_1)
         assert conn_plus_in_transaction(atomic_conn_2)
 
-    assert conn_plus_is_idle(conn_plus, isolation_level)
+    assert conn_plus_is_idle(sqlite_conn, isolation_level)
     assert conn_plus_is_idle(atomic_conn_1, isolation_level)
     assert conn_plus_is_idle(atomic_conn_2, isolation_level)
 
-    assert atomic_in_progress == conn_plus.atomic_in_progress
+    assert atomic_in_progress == sqlite_conn.atomic_in_progress
     assert atomic_in_progress == atomic_conn_1.atomic_in_progress
     assert atomic_in_progress == atomic_conn_2.atomic_in_progress
 
 
 @pytest.mark.parametrize(
     argnames="create_conn_plus",
-    argvalues=(make_connection_plus_from, ConnectionPlus),
+    argvalues=(make_connection_plus_from, ConnectionPlus),  # pyright: ignore[reportDeprecated]
     ids=("make_connection_plus_from", "ConnectionPlus"),
 )
 def test_that_use_of_atomic_commits_only_at_outermost_context(
@@ -304,19 +333,103 @@ def test_that_use_of_atomic_commits_only_at_outermost_context(
     assert 3 == len(control_conn.execute(get_all_runs).fetchall())
 
 
+def test_that_use_of_atomic_commits_only_at_outermost_context_atomic_connection(
+    tmp_path,
+) -> None:
+    """
+    This test tests the behavior of `ConnectionPlus` that is created from
+    `sqlite3.Connection` with respect to `atomic` context manager and commits.
+    """
+    dbfile = str(tmp_path / "temp.db")
+    # just initialize the database file, connection objects needed for
+    # testing in this test function are created separately, see below
+    connect(dbfile)
+
+    connection = AtomicConnection(dbfile)
+
+    # this connection is going to be used to test whether changes have been
+    # committed to the database file
+    control_conn = connect(dbfile)
+
+    get_all_runs = "SELECT * FROM runs"
+    insert_run_with_name = "INSERT INTO runs (name) VALUES (?)"
+
+    # assert that at the beginning of the test there are no runs in the
+    # table; we'll be adding new rows to the runs table below
+
+    assert 0 == len(connection.execute(get_all_runs).fetchall())
+    assert 0 == len(control_conn.execute(get_all_runs).fetchall())
+
+    # add 1 new row, and assert the state of the runs table at every step
+    # note that control_conn will only detect the change after the `atomic`
+    # context manager is exited
+
+    with atomic(connection) as atomic_conn:
+        assert 0 == len(connection.execute(get_all_runs).fetchall())
+        assert 0 == len(atomic_conn.execute(get_all_runs).fetchall())
+        assert 0 == len(control_conn.execute(get_all_runs).fetchall())
+
+        atomic_conn.cursor().execute(insert_run_with_name, ["aaa"])
+
+        assert 1 == len(connection.execute(get_all_runs).fetchall())
+        assert 1 == len(atomic_conn.execute(get_all_runs).fetchall())
+        assert 0 == len(control_conn.execute(get_all_runs).fetchall())
+
+    assert 1 == len(connection.execute(get_all_runs).fetchall())
+    assert 1 == len(atomic_conn.execute(get_all_runs).fetchall())
+    assert 1 == len(control_conn.execute(get_all_runs).fetchall())
+
+    # let's add two new rows but each inside its own `atomic` context manager
+    # we expect to see the actual change in the database only after we exit
+    # the outermost context.
+
+    with atomic(connection) as atomic_conn_1:
+        assert 1 == len(connection.execute(get_all_runs).fetchall())
+        assert 1 == len(atomic_conn_1.execute(get_all_runs).fetchall())
+        assert 1 == len(control_conn.execute(get_all_runs).fetchall())
+
+        atomic_conn_1.cursor().execute(insert_run_with_name, ["bbb"])
+
+        assert 2 == len(connection.execute(get_all_runs).fetchall())
+        assert 2 == len(atomic_conn_1.execute(get_all_runs).fetchall())
+        assert 1 == len(control_conn.execute(get_all_runs).fetchall())
+
+        with atomic(atomic_conn_1) as atomic_conn_2:
+            assert 2 == len(connection.execute(get_all_runs).fetchall())
+            assert 2 == len(atomic_conn_1.execute(get_all_runs).fetchall())
+            assert 2 == len(atomic_conn_2.execute(get_all_runs).fetchall())
+            assert 1 == len(control_conn.execute(get_all_runs).fetchall())
+
+            atomic_conn_2.cursor().execute(insert_run_with_name, ["ccc"])
+
+            assert 3 == len(connection.execute(get_all_runs).fetchall())
+            assert 3 == len(atomic_conn_1.execute(get_all_runs).fetchall())
+            assert 3 == len(atomic_conn_2.execute(get_all_runs).fetchall())
+            assert 1 == len(control_conn.execute(get_all_runs).fetchall())
+
+        assert 3 == len(connection.execute(get_all_runs).fetchall())
+        assert 3 == len(atomic_conn_1.execute(get_all_runs).fetchall())
+        assert 3 == len(atomic_conn_2.execute(get_all_runs).fetchall())
+        assert 1 == len(control_conn.execute(get_all_runs).fetchall())
+
+    assert 3 == len(connection.execute(get_all_runs).fetchall())
+    assert 3 == len(atomic_conn_1.execute(get_all_runs).fetchall())
+    assert 3 == len(atomic_conn_2.execute(get_all_runs).fetchall())
+    assert 3 == len(control_conn.execute(get_all_runs).fetchall())
+
+
 def test_atomic_transaction(tmp_path) -> None:
     """Test that atomic_transaction works for ConnectionPlus"""
     dbfile = str(tmp_path / "temp.db")
 
-    conn = ConnectionPlus(sqlite3.connect(dbfile))
-
-    ctrl_conn = sqlite3.connect(dbfile)
+    conn = AtomicConnection(dbfile)
 
     sql_create_table = "CREATE TABLE smth (name TEXT)"
-    sql_table_exists = 'SELECT sql FROM sqlite_master WHERE TYPE = "table"'
 
     atomic_transaction(conn, sql_create_table)
 
+    ctrl_conn = sqlite3.connect(dbfile)
+    sql_table_exists = 'SELECT sql FROM sqlite_master WHERE TYPE = "table"'
     assert sql_create_table in ctrl_conn.execute(sql_table_exists).fetchall()[0]
 
 
@@ -327,7 +440,7 @@ def test_atomic_transaction_on_sqlite3_connection_raises(tmp_path) -> None:
     conn = sqlite3.connect(dbfile)
 
     match_str = re.escape(
-        "atomic context manager only accepts ConnectionPlus "
+        "atomic context manager only accepts AtomicConnection or ConnectionPlus "
         "database connection objects."
     )
 
@@ -339,6 +452,6 @@ def test_connect() -> None:
     conn = connect(":memory:")
 
     assert isinstance(conn, sqlite3.Connection)
-    assert isinstance(conn, ConnectionPlus)
+    assert isinstance(conn, AtomicConnection)
     assert False is conn.atomic_in_progress
     assert None is conn.row_factory