diff --git a/src/bentoml/_internal/configuration/v1/__init__.py b/src/bentoml/_internal/configuration/v1/__init__.py
index f1ca96e3e0c..8d8fca76fea 100644
--- a/src/bentoml/_internal/configuration/v1/__init__.py
+++ b/src/bentoml/_internal/configuration/v1/__init__.py
@@ -292,4 +292,14 @@ def migration(*, override_config: dict[str, t.Any]):
             current=f"{namespace}.timeout",
             replace_with=f"{namespace}.traffic.timeout",
         )
+    for key in override_config:
+        if key.startswith("runners."):
+            runner_name = key.split(".")[1]
+            if any(key.schema == runner_name for key in _RUNNER_CONFIG):
+                continue
+            rename_fields(
+                override_config,
+                current=f"runners.{runner_name}.timeout",
+                replace_with=f"runners.{runner_name}.traffic.timeout",
+            )
     return unflatten(override_config)
diff --git a/tests/unit/_internal/configuration/test_containers.py b/tests/unit/_internal/configuration/test_containers.py
index a448fad503b..2ac60c88d3f 100644
--- a/tests/unit/_internal/configuration/test_containers.py
+++ b/tests/unit/_internal/configuration/test_containers.py
@@ -152,9 +152,12 @@ def test_runner_timeouts(container_from_file: t.Callable[[str], ConfigDictType])
             timeout: 100
     test_runner_2:
         resources: system
+    test_runner_3:
+        timeout: 60
 """
     bentoml_cfg = container_from_file(RUNNER_TIMEOUTS)
     runner_cfg = bentoml_cfg["runners"]
     assert runner_cfg["traffic"]["timeout"] == 50
     assert runner_cfg["test_runner_1"]["traffic"]["timeout"] == 100
     assert runner_cfg["test_runner_2"]["traffic"]["timeout"] == 50
+    assert runner_cfg["test_runner_3"]["traffic"]["timeout"] == 60