diff --git a/pkg-r/NEWS.md b/pkg-r/NEWS.md
index d157e533..c9b28036 100644
--- a/pkg-r/NEWS.md
+++ b/pkg-r/NEWS.md
@@ -1,5 +1,7 @@
 # querychat (development version)
 
+* `querychat_app()` will now only automatically clean up the data source if QueryChat creates the data source internally from a data frame. (#164)
+
 * **Breaking change:** The `$sql()` method now returns `NULL` instead of `""` (empty string) when no query has been set, aligning with the behavior of `$title()` for consistency. Most code using `isTruthy()` or similar falsy checks will continue working without changes. Code that explicitly checks `sql() == ""` should be updated to use falsy checks (e.g., `!isTruthy(sql())`) or explicit null checks (`is.null(sql())`). (#146)
 
 * Tool detail cards can now be expanded or collapsed by default when querychat runs a query or updates the dashboard via the `querychat.tool_details` R option or the `QUERYCHAT_TOOL_DETAILS` environment variable. Valid values are `"expanded"`, `"collapsed"`, or `"default"`. (#137)
diff --git a/pkg-r/R/QueryChat.R b/pkg-r/R/QueryChat.R
index 6ed12a8d..47e7338b 100644
--- a/pkg-r/R/QueryChat.R
+++ b/pkg-r/R/QueryChat.R
@@ -166,9 +166,6 @@ QueryChat <- R6::R6Class(
 
       private$.data_source <- normalize_data_source(data_source, table_name)
 
-      # Validate table name
-      check_sql_table_name(table_name)
-
       self$id <- id %||% table_name
 
       if (!is.null(greeting) && file.exists(greeting)) {
@@ -192,7 +189,7 @@ QueryChat <- R6::R6Class(
 
       # By default, only close automatically if a Shiny session is active
       if (is.na(cleanup)) {
-        cleanup <- !is.null(shiny::getDefaultReactiveDomain())
+        cleanup <- shiny::isRunning()
       }
 
       if (cleanup) {
@@ -585,8 +582,11 @@ QueryChat <- R6::R6Class(
 #'   used. See the package prompts directory for the default template format.
 #' @param cleanup Whether or not to automatically run `$cleanup()` when the
 #'   Shiny session/app stops. By default, cleanup only occurs if `QueryChat`
-#'   gets created within a Shiny session. Set to `TRUE` to always clean up,
-#'   or `FALSE` to never clean up automatically.
+#'   is created within a Shiny app. Set to `TRUE` to always clean up, or
+#'   `FALSE` to never clean up automatically.
+#'
+#'   In `querychat_app()`, in-memory databases created for data frames are
+#'   always cleaned up.
 #'
 #' @return A `QueryChat` object. See [QueryChat] for available methods.
 #'
@@ -668,13 +668,26 @@ querychat_app <- function(
   categorical_threshold = 20,
   extra_instructions = NULL,
   prompt_template = NULL,
-  cleanup = TRUE,
+  cleanup = NA,
   bookmark_store = "url"
 ) {
+  if (shiny::isRunning()) {
+    cli::cli_abort(
+      "{.fn querychat_app} cannot be called from within a Shiny app. Use {.fn querychat} instead."
+    )
+  }
+
   if (is_missing(table_name) && is.data.frame(data_source)) {
     table_name <- deparse1(substitute(data_source))
   }
 
+  check_bool(cleanup, allow_na = TRUE)
+  if (is.data.frame(data_source)) {
+    cleanup <- TRUE
+  } else if (is.na(cleanup)) {
+    cleanup <- FALSE
+  }
+
   qc <- QueryChat$new(
     data_source = data_source,
     table_name = table_name,
@@ -697,6 +710,8 @@ normalize_data_source <- function(data_source, table_name) {
     return(data_source)
   }
 
+  check_sql_table_name(table_name, call = caller_env())
+
   if (is.data.frame(data_source)) {
     return(DataFrameSource$new(data_source, table_name))
   }
diff --git a/pkg-r/R/utils-shiny.R b/pkg-r/R/utils-shiny.R
new file mode 100644
index 00000000..893a57a1
--- /dev/null
+++ b/pkg-r/R/utils-shiny.R
@@ -0,0 +1,3 @@
+in_shiny_session <- function() {
+  !is.null(shiny::getDefaultReactiveDomain()) # nocov
+}
diff --git a/pkg-r/man/querychat-convenience.Rd b/pkg-r/man/querychat-convenience.Rd
index f07c03e4..2e176f08 100644
--- a/pkg-r/man/querychat-convenience.Rd
+++ b/pkg-r/man/querychat-convenience.Rd
@@ -30,7 +30,7 @@ querychat_app(
   categorical_threshold = 20,
   extra_instructions = NULL,
   prompt_template = NULL,
-  cleanup = TRUE,
+  cleanup = NA,
   bookmark_store = "url"
 )
 }
@@ -81,8 +81,11 @@ used. See the package prompts directory for the default template format.}
 
 \item{cleanup}{Whether or not to automatically run \verb{$cleanup()} when the
 Shiny session/app stops. By default, cleanup only occurs if \code{QueryChat}
-gets created within a Shiny session. Set to \code{TRUE} to always clean up,
-or \code{FALSE} to never clean up automatically.}
+is created within a Shiny app. Set to \code{TRUE} to always clean up, or
+\code{FALSE} to never clean up automatically.
+
+In \code{querychat_app()}, in-memory databases created for data frames are
+always cleaned up.}
 
 \item{bookmark_store}{The bookmarking storage method. Passed to
 \code{\link[shiny:enableBookmarking]{shiny::enableBookmarking()}}. If \code{"url"} or \code{"server"}, the chat state
diff --git a/pkg-r/man/querychat-package.Rd b/pkg-r/man/querychat-package.Rd
index 63598eda..7c10e48a 100644
--- a/pkg-r/man/querychat-package.Rd
+++ b/pkg-r/man/querychat-package.Rd
@@ -75,11 +75,19 @@ Useful links:
 \itemize{
   \item \url{https://posit-dev.github.io/querychat/pkg-r}
   \item \url{https://posit-dev.github.io/querychat}
+  \item \url{https://github.com/posit-dev/querychat}
+  \item Report bugs at \url{https://github.com/posit-dev/querychat/issues}
 }
 
 }
 \author{
-\strong{Maintainer}: Joe Cheng \email{joe@posit.co}
+\strong{Maintainer}: Garrick Aden-Buie \email{garrick@posit.co} (\href{https://orcid.org/0000-0002-7111-0077}{ORCID})
+
+Authors:
+\itemize{
+  \item Joe Cheng \email{joe@posit.co} [conceptor]
+  \item Carson Sievert \email{carson@posit.co} (\href{https://orcid.org/0000-0002-4958-2844}{ORCID})
+}
 
 Other contributors:
 \itemize{
diff --git a/pkg-r/tests/testthat/test-QueryChat.R b/pkg-r/tests/testthat/test-QueryChat.R
index 91eb3847..526a41b6 100644
--- a/pkg-r/tests/testthat/test-QueryChat.R
+++ b/pkg-r/tests/testthat/test-QueryChat.R
@@ -306,3 +306,39 @@ describe("normalize_data_source()", {
     })
   })
 })
+
+test_that("querychat_app() only cleans up data frame sources on exit", {
+  local_mocked_r6_class(
+    QueryChat,
+    public = list(
+      initialize = function(..., cleanup) {
+        # have to use an option because the code is evaluated in a far-away env
+        options(.test_cleanup = cleanup)
+      },
+      app = function(...) {}
+    )
+  )
+  withr::local_options(rlang_interactive = TRUE)
+
+  withr::with_options(list(.test_cleanup = NULL), {
+    test_df <- new_test_df()
+    querychat_app(test_df)
+    cleanup_result <- getOption(".test_cleanup")
+    expect_true(cleanup_result)
+  })
+
+  withr::with_options(list(.test_cleanup = NULL), {
+    test_ds <- local_data_frame_source(new_test_df())
+    querychat_app(test_ds)
+    cleanup_result <- getOption(".test_cleanup")
+    expect_false(cleanup_result)
+  })
+
+  withr::with_options(list(.test_cleanup = NULL), {
+    con <- local_sqlite_connection(new_test_df())
+    test_ds <- DBISource$new(con$conn, "test_table")
+    querychat_app(test_ds)
+    cleanup_result <- getOption(".test_cleanup")
+    expect_false(cleanup_result)
+  })
+})