diff --git a/backend/open_webui/utils/middleware.py b/backend/open_webui/utils/middleware.py
index bff0626a9..630ab608c 100644
--- a/backend/open_webui/utils/middleware.py
+++ b/backend/open_webui/utils/middleware.py
@@ -2158,14 +2158,17 @@ async def process_chat_payload(request, form_data, user, metadata, model):
                 )
 
         if "code_interpreter" in features and features["code_interpreter"]:
-            form_data["messages"] = add_or_update_user_message(
-                (
-                    request.app.state.config.CODE_INTERPRETER_PROMPT_TEMPLATE
-                    if request.app.state.config.CODE_INTERPRETER_PROMPT_TEMPLATE != ""
-                    else DEFAULT_CODE_INTERPRETER_PROMPT
-                ),
-                form_data["messages"],
-            )
+            # Skip XML-tag prompt injection when native FC is enabled —
+            # execute_code will be injected as a builtin tool instead
+            if metadata.get("params", {}).get("function_calling") != "native":
+                form_data["messages"] = add_or_update_user_message(
+                    (
+                        request.app.state.config.CODE_INTERPRETER_PROMPT_TEMPLATE
+                        if request.app.state.config.CODE_INTERPRETER_PROMPT_TEMPLATE != ""
+                        else DEFAULT_CODE_INTERPRETER_PROMPT
+                    ),
+                    form_data["messages"],
+                )
 
     tool_ids = form_data.pop("tool_ids", None)
     files = form_data.pop("files", None)