diff --git a/litellm/__init__.py b/litellm/__init__.py
index 922a0afcedef..35fa2629d1c1 100644
--- a/litellm/__init__.py
+++ b/litellm/__init__.py
@@ -813,7 +813,10 @@ def add_known_models():
 from .cost_calculator import completion_cost
 from litellm.litellm_core_utils.litellm_logging import Logging, modify_integration
 from litellm.litellm_core_utils.get_llm_provider_logic import get_llm_provider
-from litellm.litellm_core_utils.core_helpers import remove_index_from_tool_calls
+from litellm.litellm_core_utils.core_helpers import (
+    remove_index_from_tool_calls,
+    remove_items_at_indices,
+)
 from litellm.litellm_core_utils.token_counter import get_modified_max_tokens
 from .utils import (
     client,
diff --git a/litellm/litellm_core_utils/core_helpers.py b/litellm/litellm_core_utils/core_helpers.py
index 28a0097c30de..a57496f17f16 100644
--- a/litellm/litellm_core_utils/core_helpers.py
+++ b/litellm/litellm_core_utils/core_helpers.py
@@ -1,6 +1,6 @@
 # What is this?
 ## Helper utilities
-from typing import TYPE_CHECKING, Any, List, Optional, Union
+from typing import TYPE_CHECKING, Any, List, Optional, Union, Iterable
 
 import httpx
 
@@ -67,7 +67,16 @@ def remove_index_from_tool_calls(
                     ):  # Type guard to ensure it's a dict
                         tool_call.pop("index", None)
 
-    return
+        return
+
+
+def remove_items_at_indices(items: Optional[List[Any]], indices: Iterable[int]) -> None:
+    """Remove items from a list in-place by index"""
+    if items is None:
+        return
+    for index in sorted(set(indices), reverse=True):
+        if 0 <= index < len(items):
+            items.pop(index)
 
 
 def add_missing_spend_metadata_to_litellm_metadata(
diff --git a/litellm/vector_stores/vector_store_registry.py b/litellm/vector_stores/vector_store_registry.py
index a045406d78a2..78dd8ffd5a4c 100644
--- a/litellm/vector_stores/vector_store_registry.py
+++ b/litellm/vector_stores/vector_store_registry.py
@@ -3,6 +3,8 @@
 from datetime import datetime, timezone
 from typing import TYPE_CHECKING, Any, Dict, List, Optional
 
+from litellm.litellm_core_utils.core_helpers import remove_items_at_indices
+
 from litellm._logging import verbose_logger
 from litellm.types.vector_stores import (
     LiteLLM_ManagedVectorStore,
@@ -55,9 +57,26 @@ def pop_vector_store_ids_to_run(
         vector_store_ids = non_default_params.pop("vector_store_ids", None) or []
 
         # 2. check if vector_store_ids is provided as a tool in the request
-        vector_store_ids = self._get_vector_store_ids_from_tool_calls(
-            tools=tools, vector_store_ids=vector_store_ids
-        )
+        if tools:
+            tools_to_remove: List[int] = []
+            for i, tool in enumerate(tools):
+                tool_vector_store_ids: List[str] = tool.get("vector_store_ids", [])
+                if len(tool_vector_store_ids) == 0:
+                    continue
+
+                vector_store_ids.extend(tool_vector_store_ids)
+
+                # remove the tool if all vector_store_ids are recognised in the registry
+                recognised = all(
+                    any(vs.get("vector_store_id") == vs_id for vs in self.vector_stores)
+                    for vs_id in tool_vector_store_ids
+                )
+                if recognised:
+                    tools_to_remove.append(i)
+
+            # remove recognised tools from the original list
+            remove_items_at_indices(tools, tools_to_remove)
+
         return vector_store_ids
 
     def get_vector_store_to_run(
diff --git a/tests/logging_callback_tests/test_bedrock_knowledgebase_hook.py b/tests/logging_callback_tests/test_bedrock_knowledgebase_hook.py
index a8afe9ebbaa1..5706de85030b 100644
--- a/tests/logging_callback_tests/test_bedrock_knowledgebase_hook.py
+++ b/tests/logging_callback_tests/test_bedrock_knowledgebase_hook.py
@@ -161,9 +161,12 @@ async def test_openai_with_knowledge_base_mock_openai(setup_vector_store_registr
         # Verify the API was called
         mock_client.assert_called_once()
         request_body = mock_client.call_args.kwargs
-        
+
         # Verify the request contains messages with knowledge base context
         assert "messages" in request_body
+        # The original tools field should be removed once the vector store ids
+        # have been processed by LiteLLM.
+        assert "tools" not in request_body
         messages = request_body["messages"]
         
         # We expect at least 2 messages: