diff --git a/backend/open_webui/routers/files.py b/backend/open_webui/routers/files.py
index facf032fc5..7900baa495 100644
--- a/backend/open_webui/routers/files.py
+++ b/backend/open_webui/routers/files.py
@@ -260,11 +260,12 @@ async def upload_file_handler(
                         **({'status': 'pending'} if process else {}),
                     },
                     'meta': {
-                        # Store original filename with path for sync comparison
-                        'name': unsanitized_filename,
+                        'name': name,
                         'content_type': (file.content_type if isinstance(file.content_type, str) else None),
                         'size': len(contents),
                         'file_hash': file_hash,
+                        # Store original path for directory sync (includes subdirectories)
+                        'original_path': unsanitized_filename,
                         'data': file_metadata,
                     },
                 }
diff --git a/backend/open_webui/routers/knowledge.py b/backend/open_webui/routers/knowledge.py
index b648a8824e..977a774261 100644
--- a/backend/open_webui/routers/knowledge.py
+++ b/backend/open_webui/routers/knowledge.py
@@ -1167,12 +1167,16 @@ async def compare_files_for_sync(
     # Get all files currently in the knowledge base
     existing_files = await Knowledges.get_files_by_id(id, db=db)
 
-    # Build a map of existing files by filename for quick lookup
-    existing_by_filename: dict[str, FileModel] = {}
+    # Build a map of existing files by their sync path for quick lookup
+    # Priority: original_path (for directory sync) > name > filename
+    existing_by_path: dict[str, FileModel] = {}
     for file in existing_files:
-        # Use the original filename from meta if available, otherwise use filename field
-        filename = file.meta.get('name', file.filename) if file.meta else file.filename
-        existing_by_filename[filename] = file
+        if file.meta:
+            # Use original_path for sync comparison (includes subdirectory structure)
+            sync_path = file.meta.get('original_path') or file.meta.get('name', file.filename)
+        else:
+            sync_path = file.filename
+        existing_by_path[sync_path] = file
 
     # Track files from the incoming directory
     incoming_filenames = set()
@@ -1185,7 +1189,7 @@ async def compare_files_for_sync(
         incoming_filenames.add(incoming_file.file_path)
 
         # Check if file exists in knowledge base
-        existing_file = existing_by_filename.get(incoming_file.file_path)
+        existing_file = existing_by_path.get(incoming_file.file_path)
 
         if existing_file:
             # Check if hash is already stored in meta (files uploaded after this feature)
@@ -1228,8 +1232,8 @@ async def compare_files_for_sync(
             new_files.append(incoming_file.file_path)
 
     # Find files to delete (exist in KB but not in incoming directory)
-    for filename, file in existing_by_filename.items():
-        if filename not in incoming_filenames:
+    for sync_path, file in existing_by_path.items():
+        if sync_path not in incoming_filenames:
             removed_file_ids.append(file.id)