diff --git a/litellm/proxy/_lazy_openapi_snapshot.py b/litellm/proxy/_lazy_openapi_snapshot.py
index c63ff8d0733..a9d5396cc29 100644
--- a/litellm/proxy/_lazy_openapi_snapshot.py
+++ b/litellm/proxy/_lazy_openapi_snapshot.py
@@ -86,7 +86,6 @@ def generate_snapshot() -> Dict[str, Dict]:
     import importlib
 
     from fastapi.openapi.utils import get_openapi
-
     from litellm.proxy._lazy_features import LAZY_FEATURES
     from litellm.proxy.proxy_server import app, ensure_unique_openapi_operation_ids
 
@@ -133,7 +132,6 @@ def generate_snapshot() -> Dict[str, Dict]:
         }
     return fragments
 
-
 if __name__ == "__main__":
     fragments = generate_snapshot()
     SNAPSHOT_FILE.write_text(json.dumps(fragments, indent=2, sort_keys=True) + "\n")
diff --git a/litellm/proxy/hooks/mcp_semantic_filter/hook.py b/litellm/proxy/hooks/mcp_semantic_filter/hook.py
index e05e346e3f9..645e0eb84aa 100644
--- a/litellm/proxy/hooks/mcp_semantic_filter/hook.py
+++ b/litellm/proxy/hooks/mcp_semantic_filter/hook.py
@@ -5,6 +5,7 @@ Pre-call hook that filters MCP tools semantically before LLM inference.
 Reduces context window size and improves tool selection accuracy.
 """
 
+from collections import Counter
 from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
 
 from litellm._logging import verbose_proxy_logger
@@ -177,6 +178,30 @@ class SemanticToolFilterHook(CustomLogger):
 
         return native_tools, mcp_tools
 
+    def _merge_filtered_tools_preserving_request_order(
+        self,
+        tools: List[Any],
+        filtered_mcp_tools: List[Any],
+    ) -> List[Any]:
+        filtered_mcp_tool_counts = Counter(
+            tool_name
+            for tool in filtered_mcp_tools
+            if (tool_name := self._get_tool_name(tool))
+        )
+        filtered_tools: List[Any] = []
+
+        for tool in tools:
+            if not self._is_mcp_router_tool(tool):
+                filtered_tools.append(tool)
+                continue
+
+            tool_name = self._get_tool_name(tool)
+            if filtered_mcp_tool_counts[tool_name] > 0:
+                filtered_tools.append(tool)
+                filtered_mcp_tool_counts[tool_name] -= 1
+
+        return filtered_tools
+
     async def async_pre_call_hook(
         self,
         user_api_key_dict: "UserAPIKeyAuth",
@@ -272,7 +297,7 @@ class SemanticToolFilterHook(CustomLogger):
                 f"with query: '{user_query[:50]}...'"
             )
 
-            native_tools, mcp_tools = self._partition_mcp_router_tools(tools)
+            _, mcp_tools = self._partition_mcp_router_tools(tools)
             if not mcp_tools:
                 verbose_proxy_logger.debug(
                     "No MCP router tools in request, skipping semantic filter"
@@ -284,7 +309,9 @@ class SemanticToolFilterHook(CustomLogger):
                 query=user_query,
                 available_tools=mcp_tools,  # type: ignore
             )
-            filtered_tools = native_tools + filtered_mcp_tools
+            filtered_tools = self._merge_filtered_tools_preserving_request_order(
+                tools, filtered_mcp_tools
+            )
 
             # Always update tools and emit header (even if count unchanged)
             data["tools"] = filtered_tools
diff --git a/tests/test_litellm/proxy/_experimental/mcp_server/test_semantic_tool_filter.py b/tests/test_litellm/proxy/_experimental/mcp_server/test_semantic_tool_filter.py
index 2fdd95e65fa..49dda138977 100644
--- a/tests/test_litellm/proxy/_experimental/mcp_server/test_semantic_tool_filter.py
+++ b/tests/test_litellm/proxy/_experimental/mcp_server/test_semantic_tool_filter.py
@@ -558,6 +558,65 @@ async def test_semantic_filter_hook_preserves_native_openai_tools():
     )
 
 
+@pytest.mark.asyncio
+async def test_semantic_filter_hook_preserves_remaining_tool_order():
+    """
+    Filtering MCP router tools should not reorder caller-owned native tools
+    around the MCP tools that survive semantic filtering.
+    """
+    from litellm.proxy._experimental.mcp_server.semantic_tool_filter import (
+        SemanticMCPToolFilter,
+    )
+    from litellm.proxy.hooks.mcp_semantic_filter import SemanticToolFilterHook
+
+    filter_instance = SemanticMCPToolFilter(
+        embedding_model="text-embedding-3-small",
+        litellm_router_instance=Mock(),
+        top_k=3,
+        similarity_threshold=0.3,
+        enabled=True,
+    )
+    mcp_search_tool = {"name": "github-search", "description": "Search GitHub"}
+    mcp_issue_tool = {"name": "github-issue", "description": "Create GitHub issue"}
+    filter_instance._tool_map = {
+        mcp_search_tool["name"]: mcp_search_tool,
+        mcp_issue_tool["name"]: mcp_issue_tool,
+    }
+    filter_instance.filter_tools = AsyncMock(  # type: ignore[method-assign]
+        return_value=[mcp_issue_tool, mcp_search_tool]
+    )
+
+    native_tool = {
+        "type": "function",
+        "function": {
+            "name": "weather_lookup",
+            "description": "Look up weather for a city",
+            "parameters": {"type": "object"},
+        },
+    }
+    hook = SemanticToolFilterHook(filter_instance)
+    data = {
+        "model": "gpt-4",
+        "messages": [{"role": "user", "content": "Search GitHub"}],
+        "tools": [mcp_search_tool, native_tool, mcp_issue_tool],
+        "metadata": {},
+    }
+
+    result = await hook.async_pre_call_hook(
+        user_api_key_dict=Mock(),
+        cache=Mock(),
+        data=data,
+        call_type="completion",
+    )
+
+    assert result is data
+    assert result["tools"] == [mcp_search_tool, native_tool, mcp_issue_tool]
+    assert (
+        result["metadata"]["litellm_semantic_filter_tools"]
+        == "github-search,weather_lookup,github-issue"
+    )
+
+
 @pytest.mark.asyncio
 async def test_semantic_filter_hook_skips_all_native_openai_tools():
     """