diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
index b0470b0813e3..13042e76254c 100644
--- a/lib/galaxy/managers/hdas.py
+++ b/lib/galaxy/managers/hdas.py
@@ -406,17 +406,16 @@ def cleanup_items(self, user: model.User, item_ids: Set[int]) -> StorageItemsCle
         total_free_bytes = 0
         errors: List[StorageItemCleanupError] = []
 
-        for hda_id in item_ids:
-            try:
-                hda = self.hda_manager.get_owned(hda_id, user)
-                self.hda_manager.purge(hda)
-                success_item_count += 1
-                total_free_bytes += int(hda.get_size())
-            except BaseException as e:
-                errors.append(StorageItemCleanupError(item_id=hda_id, error=str(e)))
-
-        if success_item_count:
-            self.hda_manager.session().flush()
+        with self.hda_manager.session().begin():
+            for hda_id in item_ids:
+                try:
+                    hda = self.hda_manager.get_owned(hda_id, user)
+                    self.hda_manager.purge(hda)
+                    success_item_count += 1
+                    total_free_bytes += int(hda.get_size())
+                except BaseException as e:
+                    errors.append(StorageItemCleanupError(item_id=hda_id, error=str(e)))
+
         return StorageItemsCleanupResult(
             total_item_count=len(item_ids),
             success_item_count=success_item_count,
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index 9aa5868720a6..98be1ed04880 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -415,17 +415,16 @@ def cleanup_items(self, user: model.User, item_ids: Set[int]) -> StorageItemsCle
         total_free_bytes = 0
         errors: List[StorageItemCleanupError] = []
 
-        for history_id in item_ids:
-            try:
-                history = self.history_manager.get_owned(history_id, user)
-                self.history_manager.purge(history, flush=False)
-                success_item_count += 1
-                total_free_bytes += int(history.disk_size)
-            except BaseException as e:
-                errors.append(StorageItemCleanupError(item_id=history_id, error=str(e)))
-
-        if success_item_count:
-            self.history_manager.session().flush()
+        with self.history_manager.session().begin():
+            for history_id in item_ids:
+                try:
+                    history = self.history_manager.get_owned(history_id, user)
+                    self.history_manager.purge(history, flush=False)
+                    success_item_count += 1
+                    total_free_bytes += int(history.disk_size)
+                except BaseException as e:
+                    errors.append(StorageItemCleanupError(item_id=history_id, error=str(e)))
+
         return StorageItemsCleanupResult(
             total_item_count=len(item_ids),
             success_item_count=success_item_count,