diff --git a/src/paperless_ai/tests/test_vector_store.py b/src/paperless_ai/tests/test_vector_store.py
index 8e2f1a7a7..2633e513f 100644
--- a/src/paperless_ai/tests/test_vector_store.py
+++ b/src/paperless_ai/tests/test_vector_store.py
@@ -145,6 +145,7 @@ class TestPaperlessLanceVectorStoreCrud:
         assert store.table_exists() is False
 
     def test_build_where_or_condition(self) -> None:
+
         from llama_index.core.vector_stores.types import FilterCondition
 
         from paperless_ai.vector_store import _build_where
@@ -167,3 +168,43 @@ class TestPaperlessLanceVectorStoreCrud:
             ),
         )
         assert where == "document_id = '1' OR document_id = '2'"
+
+
+class TestPaperlessLanceVectorStoreUpsert:
+    @pytest.fixture
+    def store(self, tmp_path: Path) -> PaperlessLanceVectorStore:
+        s = PaperlessLanceVectorStore(uri=str(tmp_path / "idx"))
+        s.add(
+            [
+                _node("1-0", "1", "old0", 0.1),
+                _node("1-1", "1", "old1", 0.2),
+                _node("1-2", "1", "old2", 0.3),
+                _node("2-0", "2", "keep", 0.9),
+            ],
+        )
+        return s
+
+    def test_upsert_prunes_stale_chunks_and_keeps_others(
+        self,
+        store: PaperlessLanceVectorStore,
+    ) -> None:
+        store.upsert_document(
+            "1",
+            [_node("1-0", "1", "new0", 0.1), _node("1-1", "1", "new1", 0.2)],
+        )
+
+        table = store.client.open_table("documents")
+        doc1 = sorted(
+            r["id"] for r in table.search().where("document_id = '1'").to_list()
+        )
+        assert doc1 == ["1-0", "1-1"]  # 1-2 pruned
+        assert table.count_rows() == 3  # 2 new doc1 + 1 doc2
+
+    def test_upsert_is_single_commit(
+        self,
+        store: PaperlessLanceVectorStore,
+    ) -> None:
+        table = store.client.open_table("documents")
+        before = table.version
+        store.upsert_document("1", [_node("1-0", "1", "new0", 0.1)])
+        assert store.client.open_table("documents").version == before + 1
diff --git a/src/paperless_ai/vector_store.py b/src/paperless_ai/vector_store.py
index 96bd31e66..67b242176 100644
--- a/src/paperless_ai/vector_store.py
+++ b/src/paperless_ai/vector_store.py
@@ -129,6 +129,39 @@ class PaperlessLanceVectorStore(BasePydanticVectorStore):
             self._table.add(rows)
         return [node.node_id for node in nodes]
 
+    def upsert_document(self, document_id: str, nodes: list[BaseNode]) -> list[str]:
+        """Atomically replace all stored chunks of ``document_id`` with ``nodes``.
+
+        A single ``merge_insert`` commit: matching node ids are updated, new ids
+        inserted, and any existing rows for this document that are not in the new
+        set are deleted (``when_not_matched_by_source_delete``). This prunes stale
+        trailing chunks when an edit reduces a document's chunk count, with no
+        transient empty state for concurrent lock-free readers.
+        """
+        if not nodes:
+            # No indexable content: treat as a removal.
+            self.delete(document_id)
+            return []
+        rows = [self._row(node) for node in nodes]
+        if self._table is None:
+            dim = len(nodes[0].get_embedding())
+            self._table = self._conn.create_table(
+                self._table_name,
+                rows,
+                schema=self._schema(dim),
+            )
+            return [node.node_id for node in nodes]
+        (
+            self._table.merge_insert("id")
+            .when_matched_update_all()
+            .when_not_matched_insert_all()
+            .when_not_matched_by_source_delete(
+                f"document_id = '{_escape(document_id)}'",
+            )
+            .execute(rows)
+        )
+        return [node.node_id for node in nodes]
+
     def delete(self, ref_doc_id: str, **delete_kwargs: Any) -> None:
         if self._table is not None:
             self._table.delete(f"doc_id = '{_escape(ref_doc_id)}'")