diff --git a/nipoppy_cli/nipoppy/workflows/pipeline.py b/nipoppy_cli/nipoppy/workflows/pipeline.py
index cb033bbd..d4c04799 100644
--- a/nipoppy_cli/nipoppy/workflows/pipeline.py
+++ b/nipoppy_cli/nipoppy/workflows/pipeline.py
@@ -357,12 +357,6 @@ def run_main(self, **kwargs):
                     f": {exception}"
                 )
 
-    def run_cleanup(self, **kwargs):
-        """Run pipeline cleanup."""
-        if self.dpath_pipeline_work.exists():
-            self.rm(self.dpath_pipeline_work)
-        return super().run_cleanup(**kwargs)
-
     @abstractmethod
     def get_participants_sessions_to_run(
         self, participant_id: Optional[str], session_id: Optional[str]
diff --git a/nipoppy_cli/nipoppy/workflows/runner.py b/nipoppy_cli/nipoppy/workflows/runner.py
index e207ddc7..5e032645 100644
--- a/nipoppy_cli/nipoppy/workflows/runner.py
+++ b/nipoppy_cli/nipoppy/workflows/runner.py
@@ -208,6 +208,7 @@ def run_single(self, participant_id: str, session_id: str):
 
     def run_cleanup(self, **kwargs):
         """Run pipeline runner cleanup."""
-        if self.dpath_pipeline_bids_db.exists():
-            self.rm(self.dpath_pipeline_bids_db)
+        for dpath in [self.dpath_pipeline_bids_db, self.dpath_pipeline_work]:
+            if dpath.exists():
+                self.rm(dpath)
         return super().run_cleanup(**kwargs)
diff --git a/nipoppy_cli/tests/test_workflow_runner.py b/nipoppy_cli/tests/test_workflow_runner.py
index aa06bf7d..3444f231 100644
--- a/nipoppy_cli/tests/test_workflow_runner.py
+++ b/nipoppy_cli/tests/test_workflow_runner.py
@@ -83,6 +83,23 @@ def test_run_setup(config: Config, tmp_path: Path):
     assert runner.dpath_pipeline_work.exists()
 
 
+def test_run_cleanup(tmp_path: Path):
+    runner = PipelineRunner(
+        dpath_root=tmp_path / "my_dataset",
+        pipeline_name="dummy_pipeline",
+        pipeline_version="1.0.0",
+    )
+    dpaths = [
+        runner.dpath_pipeline_bids_db,
+        runner.dpath_pipeline_work,
+    ]
+    for dpath in dpaths:
+        dpath.mkdir(parents=True)
+    runner.run_cleanup()
+    for dpath in dpaths:
+        assert not dpath.exists()
+
+
 @pytest.mark.parametrize("simulate", [True, False])
 def test_launch_boutiques_run(simulate, config: Config, tmp_path: Path):
     runner = PipelineRunner(
diff --git a/nipoppy_cli/tests/test_workflow_tracker.py b/nipoppy_cli/tests/test_workflow_tracker.py
index d8efcf10..0d4fe5bf 100644
--- a/nipoppy_cli/tests/test_workflow_tracker.py
+++ b/nipoppy_cli/tests/test_workflow_tracker.py
@@ -232,3 +232,14 @@ def test_run_cleanup(tracker: PipelineTracker, bagel: Bagel):
 
     assert tracker.layout.fpath_imaging_bagel.exists()
     assert Bagel.load(tracker.layout.fpath_imaging_bagel).equals(bagel)
+
+
+def test_run_no_create_work_directory(tracker: PipelineTracker):
+    tracker.run()
+    assert not tracker.dpath_pipeline_work.exists()
+
+
+def test_run_no_rm_work_directory(tracker: PipelineTracker):
+    tracker.dpath_pipeline_work.mkdir(parents=True)
+    tracker.run()
+    assert tracker.dpath_pipeline_work.exists()