diff --git a/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py b/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py
index 727cce0b..93aa563e 100644
--- a/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py
+++ b/projects/jupyter-server-ydoc/jupyter_server_ydoc/handlers.py
@@ -227,8 +227,6 @@ async def open(self, room_id: str) -> None:  # type:ignore[override]
         """
         On connection open.
         """
-        self.create_task(self._websocket_server.serve(self))
-
         if isinstance(self.room, DocumentRoom):
             # Close the connection if the document session expired
             session_id = self.get_query_argument("sessionId", "")
@@ -237,16 +235,20 @@ async def open(self, room_id: str) -> None:  # type:ignore[override]
                     1003,
                     f"Document session {session_id} expired. You need to reload this browser tab.",
                 )
+                return
 
             # cancel the deletion of the room if it was scheduled
             if self.room.cleaner is not None:
                 self.room.cleaner.cancel()
 
             try:
-                # Initialize the room
+                # FIX: Initialize the room BEFORE starting to serve clients.
+                # This prevents a race condition where SYNC_STEP1 is sent before
+                # the document is loaded, causing cell duplication when the client
+                # responds with SYNC_STEP2.
+                # See: https://github.com/jupyterlab/jupyterlab/issues/14031
                 async with self._room_lock(self._room_id):
                     await self.room.initialize()
-                self._emit_awareness_event(self.current_user.username, "join")
             except Exception as e:
                 _, _, file_id = decode_file_path(self._room_id)
                 file = self._file_loaders[file_id]
@@ -267,9 +269,15 @@ async def open(self, room_id: str) -> None:  # type:ignore[override]
                     self._message_queue.put_nowait(b"")
                     self._cleanup_delay = 0
                     await self._clean_room()
+                return  # Don't start serving if initialization failed
 
+            # NOW start serving - after successful initialization
+            self.create_task(self._websocket_server.serve(self))
             self._emit(LogLevel.INFO, "initialize", "New client connected.")
+            self._emit_awareness_event(self.current_user.username, "join")
         else:
+            # TransientRoom (e.g., awareness) - no initialization needed
+            self.create_task(self._websocket_server.serve(self))
             if self._room_id != "JupyterLab:globalAwareness":
                 self._emit_awareness_event(self.current_user.username, "join")
 
diff --git a/projects/jupyter-server-ydoc/jupyter_server_ydoc/rooms.py b/projects/jupyter-server-ydoc/jupyter_server_ydoc/rooms.py
index 0708f076..3eb19cde 100644
--- a/projects/jupyter-server-ydoc/jupyter_server_ydoc/rooms.py
+++ b/projects/jupyter-server-ydoc/jupyter_server_ydoc/rooms.py
@@ -140,7 +140,6 @@ async def initialize(self) -> None:
             if not read_from_source:
                 # if YStore updates and source file are out-of-sync, resync updates with source
                 if self._document.source != model["content"]:
-                    # TODO: Delete document from the store.
                     self._emit(
                         LogLevel.INFO,
                         "initialize",
@@ -151,6 +150,14 @@ async def initialize(self) -> None:
                         self._file.path,
                         self.ystore.__class__.__name__,
                     )
+                    # FIX: Clear the document content BEFORE loading from file to prevent
+                    # cell duplication. When out-of-sync is detected, the YDoc contains
+                    # content from the YStore that may have corrupted state (e.g., from
+                    # previous duplications). If we don't clear it, the set() method will
+                    # try to MERGE the YStore content with the file content instead of
+                    # REPLACING it, which causes cell duplication.
+                    # See: https://github.com/jupyterlab/jupyterlab/issues/14031
+                    self._clear_document()
                     read_from_source = True
 
             if read_from_source:
@@ -178,6 +185,28 @@ def _emit(self, level: LogLevel, action: str | None = None, msg: str | None = No
 
         self._logger.emit(schema_id=JUPYTER_COLLABORATION_EVENTS_URI, data=data)
 
+    def _clear_document(self) -> None:
+        """
+        Clears the document content to allow a clean reload from file.
+
+        This is necessary when an out-of-sync condition is detected between the
+        YStore and the file. Without clearing, the set() method would try to
+        merge the existing content with the new content, potentially causing
+        cell duplication in notebooks.
+
+        For notebooks (YNotebook), this clears the cells array. The metadata
+        and state will be properly updated by the subsequent set() call.
+        """
+        # Check if the document has a ycells attribute (notebooks)
+        if hasattr(self._document, "ycells"):
+            # Use a transaction to ensure atomic operation
+            with self._document.ydoc.transaction():
+                self._document.ycells.clear()
+            self.log.info(
+                "Cleared document content in room %s to prevent duplication",
+                self._room_id,
+            )
+
     async def stop(self) -> None:
         """
         Stop the room.