diff --git a/doc/changes/DM-55482.bugfix.md b/doc/changes/DM-55482.bugfix.md
new file mode 100644
index 00000000..0a4261b8
--- /dev/null
+++ b/doc/changes/DM-55482.bugfix.md
@@ -0,0 +1 @@
+`pipetask run` now disables implicit threading before the pipeline is built rather than just before execution, so that thread pools created during task imports and quantum graph generation are also limited.
diff --git a/python/lsst/ctrl/mpexec/cli/cmd/commands.py b/python/lsst/ctrl/mpexec/cli/cmd/commands.py
index 68c2a704..d8a2bb95 100644
--- a/python/lsst/ctrl/mpexec/cli/cmd/commands.py
+++ b/python/lsst/ctrl/mpexec/cli/cmd/commands.py
@@ -46,6 +46,7 @@
 )
 from lsst.daf.butler.cli.utils import catch_and_exit, option_section, unwrap
 from lsst.pipe.base.quantum_reports import Report
+from lsst.utils.threads import disable_implicit_threading
 
 from .. import opt as ctrlMpExecOpts
 from .. import script
@@ -194,6 +195,11 @@ def qgraph(ctx: click.Context, **kwargs: Any) -> None:
 def run(ctx: click.Context, **kwargs: Any) -> None:
     """Build and execute pipeline and quantum graph."""
     kwargs = collect_pipeline_actions(ctx, **kwargs)
+    if not kwargs.get("enable_implicit_threading"):
+        # Limit thread pools created during pipeline construction and graph
+        # generation, not just those created during execution. script.run
+        # repeats this for callers that do not go through this command.
+        disable_implicit_threading()
     with coverage_context(kwargs):
         show = ShowInfo(kwargs.pop("show", []))
         pipeline_graph_factory = script.build(**kwargs, show=show)
diff --git a/tests/test_cliCmdRun.py b/tests/test_cliCmdRun.py
new file mode 100644
index 00000000..a125469d
--- /dev/null
+++ b/tests/test_cliCmdRun.py
@@ -0,0 +1,78 @@
+# This file is part of ctrl_mpexec.
+#
+# Developed for the LSST Data Management System.
+# This product includes software developed by the LSST Project
+# (http://www.lsst.org).
+# See the COPYRIGHT file at the top-level directory of this distribution
+# for details of code ownership.
+#
+# This software is dual licensed under the GNU General Public License and also
+# under a 3-clause BSD license. Recipients may choose which of these licenses
+# to use; please see the files gpl-3.0.txt and/or bsd_license.txt,
+# respectively.  If you choose the GPL option then the following text applies
+# (but note that there is still no warranty even if you opt for BSD instead):
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""Unit tests for the ctrl_mpexec CLI run subcommand."""
+
+import unittest
+import unittest.mock
+
+from lsst.ctrl.mpexec.cli.cmd import commands
+from lsst.ctrl.mpexec.cli.pipetask import cli as pipetask_cli
+from lsst.daf.butler.cli.utils import LogCliRunner, clickResultMsg
+
+
+class RunCommandThreadingTest(unittest.TestCase):
+    """Test implicit threading handling of "pipetask run"."""
+
+    def setUp(self):
+        self.runner = LogCliRunner()
+
+    def _invoke_with_mocks(self, args: list[str]) -> tuple:
+        """Invoke the CLI with the script functions replaced by mocks that
+        share a common parent so that call order can be checked.
+        """
+        manager = unittest.mock.Mock()
+        with (
+            unittest.mock.patch.object(commands, "disable_implicit_threading", manager.disable),
+            unittest.mock.patch.object(commands.script, "build", manager.build),
+            unittest.mock.patch.object(commands.script, "qgraph", manager.qgraph),
+            unittest.mock.patch.object(commands.script, "run", manager.run),
+        ):
+            result = self.runner.invoke(pipetask_cli, args)
+        return result, manager
+
+    def test_disable_before_graph_building(self):
+        """Implicit threading must be disabled before the pipeline is built
+        so that thread pools created during task imports and graph generation
+        are already limited.
+        """
+        result, manager = self._invoke_with_mocks(["run", "-b", "repo"])
+        self.assertEqual(result.exit_code, 0, clickResultMsg(result))
+        called = [name for name, _, _ in manager.mock_calls]
+        self.assertIn("disable", called)
+        self.assertLess(called.index("disable"), called.index("build"))
+
+    def test_enable_implicit_threading(self):
+        """No early disabling when implicit threading is requested."""
+        result, manager = self._invoke_with_mocks(["run", "-b", "repo", "--enable-implicit-threading"])
+        self.assertEqual(result.exit_code, 0, clickResultMsg(result))
+        called = [name for name, _, _ in manager.mock_calls]
+        self.assertNotIn("disable", called)
+
+
+if __name__ == "__main__":
+    unittest.main()