diff --git a/src/vectorcode/common.py b/src/vectorcode/common.py
index f4fff1a6..65ce495e 100644
--- a/src/vectorcode/common.py
+++ b/src/vectorcode/common.py
@@ -12,6 +12,7 @@
 import httpx
 from chromadb.api import AsyncClientAPI
 from chromadb.api.models.AsyncCollection import AsyncCollection
+from chromadb.api.types import IncludeEnum
 from chromadb.config import APIVersion, Settings
 from chromadb.utils import embedding_functions
 
@@ -248,3 +249,15 @@ def verify_ef(collection: AsyncCollection, configs: Config):
             f"The collection was embedded with a different set of configurations: {collection_ep}. The result may be inaccurate.",
         )
     return True
+
+
+async def list_collection_files(collection: AsyncCollection) -> list[str]:
+    return list(
+        set(
+            str(c.get("path", None))
+            for c in (await collection.get(include=[IncludeEnum.metadatas])).get(
+                "metadatas"
+            )
+            or []
+        )
+    )
diff --git a/src/vectorcode/lsp_main.py b/src/vectorcode/lsp_main.py
index f6fae6d1..e26bd7b8 100644
--- a/src/vectorcode/lsp_main.py
+++ b/src/vectorcode/lsp_main.py
@@ -15,6 +15,7 @@
     exclude_paths_by_spec,
     find_exclude_specs,
     load_files_from_include,
+    remove_orphanes,
 )
 
 try:  # pragma: nocover
@@ -220,6 +221,9 @@ async def execute_command(ls: LanguageServer, args: list[str]):
                             percentage=int(100 * i / len(tasks)),
                         ),
                     )
+
+                await remove_orphanes(collection, collection_lock, stats, stats_lock)
+
                 ls.progress.end(
                     progress_token,
                     types.WorkDoneProgressEnd(
diff --git a/src/vectorcode/mcp_main.py b/src/vectorcode/mcp_main.py
index e9a9812c..86d9989c 100644
--- a/src/vectorcode/mcp_main.py
+++ b/src/vectorcode/mcp_main.py
@@ -17,6 +17,7 @@
     chunked_add,
     exclude_paths_by_spec,
     find_exclude_specs,
+    remove_orphanes,
 )
 
 try:  # pragma: nocover
@@ -157,6 +158,9 @@ async def vectorise_files(paths: list[str], project_root: str) -> dict[str, int]
     ]
     for i, task in enumerate(asyncio.as_completed(tasks), start=1):
         await task
+
+    await remove_orphanes(collection, collection_lock, stats, stats_lock)
+
     return stats.to_dict()
 
 
diff --git a/src/vectorcode/subcommands/vectorise.py b/src/vectorcode/subcommands/vectorise.py
index e1c61dbb..40ef1619 100644
--- a/src/vectorcode/subcommands/vectorise.py
+++ b/src/vectorcode/subcommands/vectorise.py
@@ -23,7 +23,12 @@
     expand_globs,
     expand_path,
 )
-from vectorcode.common import get_client, get_collection, verify_ef
+from vectorcode.common import (
+    get_client,
+    get_collection,
+    list_collection_files,
+    verify_ef,
+)
 
 logger = logging.getLogger(name=__name__)
 
@@ -155,6 +160,25 @@ async def chunked_add(
             stats.add += 1
 
 
+async def remove_orphanes(
+    collection: AsyncCollection,
+    collection_lock: Lock,
+    stats: VectoriseStats,
+    stats_lock: Lock,
+):
+    async with collection_lock:
+        paths = await list_collection_files(collection)
+        orphans = set()
+        for path in paths:
+            if isinstance(path, str) and not os.path.isfile(path):
+                orphans.add(path)
+        async with stats_lock:
+            stats.removed = len(orphans)
+        if len(orphans):
+            logger.info(f"Removing {len(orphans)} orphaned files from database.")
+            await collection.delete(where={"path": {"$in": list(orphans)}})
+
+
 def show_stats(configs: Config, stats: VectoriseStats):
     if configs.pipe:
         print(stats.to_json())
@@ -284,19 +308,7 @@ async def vectorise(configs: Config) -> int:
             print("Abort.", file=sys.stderr)
             return 1
 
-    async with collection_lock:
-        all_results = await collection.get(include=[IncludeEnum.metadatas])
-        if all_results is not None and all_results.get("metadatas"):
-            paths = (meta["path"] for meta in (all_results["metadatas"] or []))
-            orphans = set()
-            for path in paths:
-                if isinstance(path, str) and not os.path.isfile(path):
-                    orphans.add(path)
-            async with stats_lock:
-                stats.removed = len(orphans)
-            if len(orphans):
-                logger.info(f"Removing {len(orphans)} orphaned files from database.")
-                await collection.delete(where={"path": {"$in": list(orphans)}})
+    await remove_orphanes(collection, collection_lock, stats, stats_lock)
 
     show_stats(configs=configs, stats=stats)
     return 0
diff --git a/tests/test_lsp.py b/tests/test_lsp.py
index 530c2316..46bcf7eb 100644
--- a/tests/test_lsp.py
+++ b/tests/test_lsp.py
@@ -265,6 +265,9 @@ async def test_execute_command_vectorise(mock_language_server, mock_config: Conf
         patch(
             "vectorcode.lsp_main.make_caches", new_callable=AsyncMock
         ),  # Mock make_caches to avoid actual file system ops
+        patch(
+            "vectorcode.lsp_main.remove_orphanes", new_callable=AsyncMock
+        ) as mock_remove_orphanes,
     ):
         from unittest.mock import ANY
 
@@ -279,7 +282,7 @@ async def test_execute_command_vectorise(mock_language_server, mock_config: Conf
         mock_parse_cli_args.return_value = mock_config
         mock_client = AsyncMock()
         mock_get_client.return_value = mock_client
-        mock_collection = MagicMock()
+        mock_collection = AsyncMock()
         mock_get_collection.return_value = mock_collection
         mock_client.get_max_batch_size.return_value = 100  # Mock batch size
 
@@ -337,6 +340,7 @@ async def test_execute_command_vectorise(mock_language_server, mock_config: Conf
         assert mock_language_server.progress.report.call_count == len(
             dummy_expanded_files
         )
+        mock_remove_orphanes.assert_called_once()
         mock_language_server.progress.end.assert_called_once()