diff --git a/jupyter_server_documents/outputs/manager.py b/jupyter_server_documents/outputs/manager.py
index 595ba3a..ba4f1af 100644
--- a/jupyter_server_documents/outputs/manager.py
+++ b/jupyter_server_documents/outputs/manager.py
@@ -302,7 +302,7 @@ def _process_loaded_no_placeholders(self, file_id: str, nb: dict) -> dict:
             cell['outputs'] = processed_outputs
         return nb
 
-    def process_saving_notebook(self, nb: dict) -> dict:
+    def process_saving_notebook(self, nb: dict, file_id: str) -> dict:
         """Process a notebook before saving to disk.
 
         This method is called when the yroom_file_api saves notebooks.
@@ -311,6 +311,7 @@ def process_saving_notebook(self, nb: dict) -> dict:
         
         Args:
             nb (dict): The notebook dict
+            file_id (str): The file identifier
             
         Returns:
             dict: The modified file data with placeholder_outputs set to True
@@ -326,6 +327,12 @@ def process_saving_notebook(self, nb: dict) -> dict:
         # Clear outputs for all code cells, as they are saved to disk
         for cell in nb.get('cells', []):
             if cell.get('cell_type') == 'code':
+                # If outputs is already an empty list, call clear for this cell
+                if cell.get('outputs') == []:
+                    cell_id = cell.get('id')
+                    if cell_id:
+                        self.clear(file_id, cell_id)
+                
                 cell['outputs'] = []
         
         return nb
diff --git a/jupyter_server_documents/rooms/yroom_file_api.py b/jupyter_server_documents/rooms/yroom_file_api.py
index 05078d4..72eabd1 100644
--- a/jupyter_server_documents/rooms/yroom_file_api.py
+++ b/jupyter_server_documents/rooms/yroom_file_api.py
@@ -376,7 +376,7 @@ async def save(self, jupyter_ydoc: YBaseDoc):
             self._save_scheduled = False
 
             if self.file_type == "notebook":
-                content = self.outputs_manager.process_saving_notebook(content)
+                content = self.outputs_manager.process_saving_notebook(content, self.file_id)
 
             # Save the YDoc via the ContentsManager
             async with self._content_lock: