diff --git a/backend/open_webui/routers/prune.py b/backend/open_webui/routers/prune.py
index 112901118d..cd7053e7fa 100644
--- a/backend/open_webui/routers/prune.py
+++ b/backend/open_webui/routers/prune.py
@@ -1381,6 +1381,13 @@ async def prune_data(form_data: PruneDataForm, user=Depends(get_admin_user)):
     If dry_run=True (default), returns preview counts without deleting anything.
     If dry_run=False, performs actual deletion and returns True on success.
     """
+    # Acquire lock to prevent concurrent operations (including previews)
+    if not PruneLock.acquire():
+        raise HTTPException(
+            status_code=status.HTTP_409_CONFLICT,
+            detail="A prune operation is already in progress. Please wait for it to complete."
+        )
+
     try:
         # Get vector database cleaner based on configuration
         vector_cleaner = get_vector_database_cleaner()
@@ -1642,45 +1649,54 @@ async def prune_data(form_data: PruneDataForm, user=Depends(get_admin_user)):
                 warnings.append(f"Vector cleanup warning: {vector_error}")
                 log.warning(f"Vector cleanup completed with errors: {vector_error}")
 
-            # Stage 5: Audio cache cleanup
-            log.info("Cleaning audio cache")
-            cleanup_audio_cache(form_data.audio_cache_max_age_days)
+        # Use modular vector database cleanup
+        warnings = []
+        deleted_vector_count, vector_error = vector_cleaner.cleanup_orphaned_collections(
+            final_active_file_ids, final_active_kb_ids
+        )
+        if vector_error:
+            warnings.append(f"Vector cleanup warning: {vector_error}")
+            log.warning(f"Vector cleanup completed with errors: {vector_error}")
 
             # Stage 6: Database optimization (optional)
             if form_data.run_vacuum:
                 log.info("Optimizing database with VACUUM (this may take a while and lock the database)")
 
+        # Stage 6: Database optimization (optional)
+        if form_data.run_vacuum:
+            log.info("Optimizing database with VACUUM (this may take a while and lock the database)")
+
+            try:
+                with get_db() as db:
+                    db.execute(text("VACUUM"))
+                    log.info("Vacuumed main database")
+            except Exception as e:
+                log.error(f"Failed to vacuum main database: {e}")
+
+            # Vector database-specific optimization
+            if isinstance(vector_cleaner, ChromaDatabaseCleaner):
                 try:
-                    with get_db() as db:
-                        db.execute(text("VACUUM"))
-                        log.info("Vacuumed main database")
+                    with sqlite3.connect(str(vector_cleaner.chroma_db_path)) as conn:
+                        conn.execute("VACUUM")
+                        log.info("Vacuumed ChromaDB database")
                 except Exception as e:
-                    log.error(f"Failed to vacuum main database: {e}")
+                    log.error(f"Failed to vacuum ChromaDB database: {e}")
+            elif (
+                isinstance(vector_cleaner, PGVectorDatabaseCleaner)
+                and vector_cleaner.session
+            ):
+                try:
+                    vector_cleaner.session.execute(text("VACUUM ANALYZE"))
+                    vector_cleaner.session.commit()
+                    log.info("Executed VACUUM ANALYZE on PostgreSQL database")
+                except Exception as e:
+                    log.error(f"Failed to vacuum PostgreSQL database: {e}")
+        else:
+            log.info("Skipping VACUUM optimization (not enabled)")
 
-                # Vector database-specific optimization
-                if isinstance(vector_cleaner, ChromaDatabaseCleaner):
-                    try:
-                        with sqlite3.connect(str(vector_cleaner.chroma_db_path)) as conn:
-                            conn.execute("VACUUM")
-                            log.info("Vacuumed ChromaDB database")
-                    except Exception as e:
-                        log.error(f"Failed to vacuum ChromaDB database: {e}")
-                elif (
-                    isinstance(vector_cleaner, PGVectorDatabaseCleaner)
-                    and vector_cleaner.session
-                ):
-                    try:
-                        vector_cleaner.session.execute(text("VACUUM ANALYZE"))
-                        vector_cleaner.session.commit()
-                        log.info("Executed VACUUM ANALYZE on PostgreSQL database")
-                    except Exception as e:
-                        log.error(f"Failed to vacuum PostgreSQL database: {e}")
-            else:
-                log.info("Skipping VACUUM optimization (not enabled)")
-
-            # Log any warnings collected during pruning
-            if warnings:
-                log.warning(f"Data pruning completed with warnings: {'; '.join(warnings)}")
+        # Log any warnings collected during pruning
+        if warnings:
+            log.warning(f"Data pruning completed with warnings: {'; '.join(warnings)}")
 
             log.info("Data pruning completed successfully")
             return True
@@ -1695,3 +1711,6 @@ async def prune_data(form_data: PruneDataForm, user=Depends(get_admin_user)):
             status_code=status.HTTP_500_INTERNAL_SERVER_ERROR,
             detail=ERROR_MESSAGES.DEFAULT("Data pruning failed"),
         )
+    finally:
+        # Always release lock, even if operation fails
+        PruneLock.release()