diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index d2afeb82b444..3f8e33321ac2 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -2157,7 +2157,9 @@ def cleanup(self, delete_files: bool = True) -> None:
                         if e.errno != errno.ENOENT:
                             raise
             if delete_files:
-                self.object_store.delete(self.get_job(), base_dir="job_work", entire_dir=True, obj_dir=True)
+                self.object_store.delete(
+                    self.get_job(), base_dir="job_work", entire_dir=True, dir_only=True, obj_dir=True
+                )
         except Exception:
             log.exception("Unable to cleanup job %d", self.job_id)
 
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index f38860b7c2c2..b21083381da4 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -218,6 +218,7 @@ def delete(
         obj,
         entire_dir: bool = False,
         base_dir=None,
+        dir_only=False,
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
@@ -572,6 +573,7 @@ def delete(
         obj,
         entire_dir: bool = False,
         base_dir=None,
+        dir_only=False,
         extra_dir=None,
         extra_dir_at_root=False,
         alt_name=None,
@@ -582,6 +584,7 @@ def delete(
             obj,
             entire_dir=entire_dir,
             base_dir=base_dir,
+            dir_only=dir_only,
             extra_dir=extra_dir,
             extra_dir_at_root=extra_dir_at_root,
             alt_name=alt_name,