diff --git a/python/semantic_kernel/connectors/faiss.py b/python/semantic_kernel/connectors/faiss.py
index ec9ba8e22dfa..1f4c92e70226 100644
--- a/python/semantic_kernel/connectors/faiss.py
+++ b/python/semantic_kernel/connectors/faiss.py
@@ -122,6 +122,7 @@ def _create_indexes(self, index: faiss.Index | None = None, indexes: dict[str, f
             if not index.is_trained:
                 raise VectorStoreInitializationException("Index must be trained before using.")
             self.indexes[self.definition.vector_fields[0].name] = index
+            self.indexes_key_map.setdefault(self.definition.vector_fields[0].name, {})
             return
         for vector_field in self.definition.vector_fields:
             if indexes and vector_field.name in indexes:
@@ -153,6 +154,9 @@ async def ensure_collection_exists(
         This includes indexes that need training, or GPU-based indexes, since you would also
         need to build the faiss package for use with GPU's yourself.
 
+        For a new collection, supplied indexes must contain no vectors. Insert records
+        through this collection so the vectors, records, and key mappings stay aligned.
+
         Args:
             index: The index to use, this can be used when there is only one vector field.
             indexes: A dictionary of indexes, the key is the name of the vector field.
diff --git a/python/tests/unit/connectors/memory/test_faiss.py b/python/tests/unit/connectors/memory/test_faiss.py
index 07c19f98aa10..f0f4e7375ffc 100644
--- a/python/tests/unit/connectors/memory/test_faiss.py
+++ b/python/tests/unit/connectors/memory/test_faiss.py
@@ -102,6 +102,48 @@ async def test_ensure_collection_exists_custom_dict(store, data_model_def):
     await collection.ensure_collection_deleted()
 
 
+@mark.parametrize("use_index_dict", [False, True], ids=["single-index", "index-dict"])
+@mark.parametrize("index_kind", ["flat-l2", "flat-ip", "hnsw"])
+async def test_custom_index_upsert_and_search(store, data_model_def, use_index_dict, index_kind):
+    collection = store.get_collection(collection_name="test", record_type=dict, definition=data_model_def)
+    records = [
+        {"id": "first", "content": "first record", "vector": [1.0, 0.0, 0.0, 0.0, 0.0]},
+        {"id": "second", "content": "second record", "vector": [-1.0, 0.0, 0.0, 0.0, 0.0]},
+    ]
+
+    for _ in range(2):
+        if index_kind == "flat-l2":
+            index = faiss.IndexFlatL2(5)
+        elif index_kind == "flat-ip":
+            index = faiss.IndexFlatIP(5)
+        else:
+            index = faiss.IndexHNSWFlat(5, 4)
+        kwargs = {"indexes": {"vector": index}} if use_index_dict else {"index": index}
+        await collection.ensure_collection_exists(**kwargs)
+        assert collection.indexes["vector"] is index
+
+        assert await collection.upsert(records[0]) == "first"
+        key_map = collection.indexes_key_map["vector"]
+        await collection.ensure_collection_exists(**kwargs)
+        assert collection.indexes_key_map["vector"] is key_map
+        assert key_map == {"first": 0}
+        assert await collection.upsert(records[1:]) == ["second"]
+        assert key_map == {"first": 0, "second": 1}
+
+        results = await collection.search(
+            vector=records[0]["vector"], top=2, include_total_count=True, include_vectors=True
+        )
+        assert results.total_count == 2
+        assert [result.record async for result in results.results] == records
+        assert await collection.get("first", include_vectors=True) == records[0]
+        assert index.ntotal == 2
+
+        await collection.ensure_collection_deleted()
+        assert collection.indexes == {}
+        assert collection.indexes_key_map == {}
+        assert collection.inner_storage == {}
+
+
 async def test_upsert(faiss_collection):
     await faiss_collection.ensure_collection_exists()
     record = {"id": "testid", "content": "test content", "vector": [0.1, 0.2, 0.3, 0.4, 0.5]}