diff --git a/bbconf/modules/bedfiles.py b/bbconf/modules/bedfiles.py
index c04a547..047d1ec 100644
--- a/bbconf/modules/bedfiles.py
+++ b/bbconf/modules/bedfiles.py
@@ -14,6 +14,7 @@
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm import Session, aliased
 from tqdm import tqdm
+from qdrant_client.http.models import PointStruct
 
 from bbconf.config_parser.bedbaseconfig import BedBaseConfig
 from geniml.search.backends import QdrantBackend
@@ -1257,7 +1258,7 @@ def _sql_search_count(self, query: str) -> int:
             count = session.execute(statement).one()
         return count[0]
 
-    def reindex_qdrant(self) -> None:
+    def reindex_qdrant(self, batch: int = 1000) -> None:
         """
         Re-upload all files to quadrant.
         !Warning: only hg38 genome can be added to qdrant!
@@ -1265,6 +1266,8 @@ def reindex_qdrant(self) -> None:
         If you want to fully reindex/reupload to qdrant, first delete collection and create new one.
 
         Upload all files to qdrant.
+
+        :param batch: number of files to upload in one batch
         """
         bb_client = BBClient()
 
@@ -1276,6 +1279,7 @@ def reindex_qdrant(self) -> None:
         results = annotation_result.results
 
         with tqdm(total=len(results), position=0, leave=True) as pbar:
+            points_list = []
             for record in results:
                 try:
                     bed_region_set_obj = GRegionSet(bb_client.seek(record.id))
@@ -1284,14 +1288,28 @@ def reindex_qdrant(self) -> None:
 
                 pbar.set_description(f"Processing file: {record.id}")
 
-                self.upload_file_qdrant(
-                    bed_id=record.id,
-                    bed_file=bed_region_set_obj,
-                    payload=record.annotation.model_dump() if record.annotation else {},
+                file_embedding = self._embed_file(bed_region_set_obj)
+                points_list.append(
+                    PointStruct(
+                        id=record.id,
+                        vector=file_embedding.tolist()[0],
+                        payload=(
+                            record.annotation.model_dump() if record.annotation else {}
+                        ),
+                    )
                 )
-                pbar.write(f"File: {record.id} uploaded to qdrant successfully.")
+                pbar.write(f"File: {record.id} successfully indexed.")
                 pbar.update(1)
 
+        _LOGGER.info(f"Uploading points to qdrant using batches...")
+        for i in range(0, len(points_list), batch):
+            operation_info = self._config.qdrant_engine.qd_client.upsert(
+                collection_name=self._config.config.qdrant.file_collection,
+                points=points_list[i : i + batch],
+            )
+
+            assert operation_info.status == "completed"
+
         return None
 
     def delete_qdrant_point(self, identifier: str) -> None: