diff --git a/src/evaluations/benchmark.py b/src/evaluations/benchmark.py
index 4eb31835..055efda5 100644
--- a/src/evaluations/benchmark.py
+++ b/src/evaluations/benchmark.py
@@ -61,7 +61,6 @@ async def populate_db(spec: DatasetSpec) -> None:
                     metadata=payload.metadata,
                 )
                 progress.advance(task)
-            rag.store.vacuum()
 
 
 def _is_relevant_match(retrieved_uri: str | None, sample: RetrievalSample) -> bool:
diff --git a/src/haiku/rag/store/repositories/document.py b/src/haiku/rag/store/repositories/document.py
index ffc66a1b..dc31878d 100644
--- a/src/haiku/rag/store/repositories/document.py
+++ b/src/haiku/rag/store/repositories/document.py
@@ -200,6 +200,8 @@ class DocumentRepository:
                     chunk.order = order
                     await self.chunk_repository.create(chunk)
 
+            # Vacuum old versions after successful creation
+            self.store.vacuum()
             return created_doc
         except Exception:
             # Roll back to the captured versions and re-raise
@@ -230,6 +232,8 @@ class DocumentRepository:
                 updated_doc.id, docling_document
             )
 
+            # Vacuum old versions after successful update
+            self.store.vacuum()
             return updated_doc
         except Exception:
             # Roll back to the captured versions and re-raise