diff --git a/packages/cli/src/pywrangler/sync.py b/packages/cli/src/pywrangler/sync.py
index 2f1cb26..e3a9af0 100644
--- a/packages/cli/src/pywrangler/sync.py
+++ b/packages/cli/src/pywrangler/sync.py
@@ -188,6 +188,18 @@ def _install_requirements_to_vendor(requirements: list[str]) -> str | None:
         f"Installing packages into [bold]{relative_vendor_path}[/bold]...",
         extra={"markup": True},
     )
+
+    # Clear pyodide venv site-packages so stale packages from previous syncs
+    # don't carry over into python_modules.
+    pyv = get_python_version()
+    site_packages_path = (
+        f"lib/python{pyv}/site-packages" if os.name != "nt" else "Lib/site-packages"
+    )
+    pyodide_site_packages = get_pyodide_venv_path() / site_packages_path
+    if pyodide_site_packages.is_dir():
+        shutil.rmtree(pyodide_site_packages)
+        pyodide_site_packages.mkdir()
+
     with temp_requirements_file(requirements) as requirements_file:
         result = run_command(
             [
@@ -209,13 +221,8 @@ def _install_requirements_to_vendor(requirements: list[str]) -> str | None:
         if result.returncode != 0:
             return result.stdout.strip()
 
-        pyv = get_python_version()
         shutil.rmtree(vendor_path)
-
-        site_packages_path = (
-            f"lib/python{pyv}/site-packages" if os.name != "nt" else "Lib/site-packages"
-        )
-        shutil.copytree(get_pyodide_venv_path() / site_packages_path, vendor_path)
+        shutil.copytree(pyodide_site_packages, vendor_path)
 
     # Create a pyvenv.cfg file in python_modules to mark it as a virtual environment
     (vendor_path / "pyvenv.cfg").touch()
diff --git a/packages/cli/tests/test_cli.py b/packages/cli/tests/test_cli.py
index f9870f2..84483a3 100644
--- a/packages/cli/tests/test_cli.py
+++ b/packages/cli/tests/test_cli.py
@@ -270,6 +270,41 @@ def test_sync_command_integration(dependencies, test_dir):  # noqa: C901 (test c
             )
 
 
+def test_sync_removes_stale_packages(test_dir):
+    """Test that removing a dependency from pyproject.toml cleans it up from python_modules."""
+    create_test_wrangler_jsonc(test_dir, "src/worker.py")
+    sync_cmd = ["uv", "run", "pywrangler", "sync"]
+
+    # First sync: install click + six
+    create_test_pyproject(test_dir, ["click", "six"])
+    result = subprocess.run(
+        sync_cmd, capture_output=True, text=True, cwd=test_dir, check=False
+    )
+    assert result.returncode == 0, (
+        f"First sync failed: {result.stdout}\n{result.stderr}"
+    )
+
+    vendor_path = test_dir / "python_modules"
+    assert is_package_installed(vendor_path, "click")
+    assert is_package_installed(vendor_path, "six")
+
+    # Second sync: remove six, keep click
+    create_test_pyproject(test_dir, ["click"])
+    result = subprocess.run(
+        sync_cmd, capture_output=True, text=True, cwd=test_dir, check=False
+    )
+    assert result.returncode == 0, (
+        f"Second sync failed: {result.stdout}\n{result.stderr}"
+    )
+
+    assert is_package_installed(vendor_path, "click"), (
+        "click should still be installed after second sync"
+    )
+    assert not is_package_installed(vendor_path, "six"), (
+        "six should have been removed from python_modules after being dropped from dependencies"
+    )
+
+
 def test_sync_command_handles_missing_pyproject():
     """Test that the sync command correctly handles a missing pyproject.toml file."""
     import tempfile
diff --git a/packages/cli/tests/test_types.py b/packages/cli/tests/test_types.py
index 02a5612..061c6ce 100644
--- a/packages/cli/tests/test_types.py
+++ b/packages/cli/tests/test_types.py
@@ -69,5 +69,5 @@ def test_types(tmp_path):
         result = run(["uv", "run", "mypy"], capture_output=True, text=True, check=False)
         assert 'Revealed type is "js.Env"' in result.stdout
         assert 'Revealed type is "js.KVNamespace_iface"' in result.stdout
-        assert 'Revealed type is "builtins.str"' in result.stdout
+        assert 'Revealed type is "str"' in result.stdout
         assert "Success: no issues found" in result.stdout