diff --git a/main.py b/main.py
index 359605f41..54d0bfa8e 100644
--- a/main.py
+++ b/main.py
@@ -100,14 +100,14 @@ def apply_custom_paths():
     extra_model_paths_config_path = os.path.join(install_dir, "extra_model_paths.yaml")
 
     if os.path.isfile(extra_paths_config_path):
-        utils.extra_config.load_extra_path_config(extra_paths_config_path)
+        utils.extra_config.load_extra_path_config(extra_paths_config_path, allow_system_dirs=True)
         if os.path.isfile(extra_model_paths_config_path):
             logging.warning(
-                "Both extra_paths.yaml and extra_model_paths.yaml found. "
-                "extra_model_paths.yaml is deprecated; please migrate to extra_paths.yaml."
+                "Both extra_paths.yaml and extra_model_paths.yaml found; "
+                "ignoring the deprecated extra_model_paths.yaml. "
+                "Please remove or migrate its entries to extra_paths.yaml."
             )
-
-    if os.path.isfile(extra_model_paths_config_path):
+    elif os.path.isfile(extra_model_paths_config_path):
         utils.extra_config.load_extra_path_config(extra_model_paths_config_path)
 
     if args.extra_model_paths_config:
diff --git a/tests-unit/utils/extra_config_test.py b/tests-unit/utils/extra_config_test.py
index baa9e1d22..1112320d9 100644
--- a/tests-unit/utils/extra_config_test.py
+++ b/tests-unit/utils/extra_config_test.py
@@ -429,7 +429,7 @@ def test_system_dir_keys(mock_yaml_load, save_restore_system_dirs, tmp_path):
     with open(yaml_path, "w") as f:
         f.write("")
 
-    load_extra_path_config(yaml_path)
+    load_extra_path_config(yaml_path, allow_system_dirs=True)
 
     assert folder_paths.get_output_directory() == os.path.normpath(str(tmp_path / "my_output"))
     assert folder_paths.get_input_directory() == os.path.normpath(str(tmp_path / "my_input"))
@@ -437,6 +437,28 @@ def test_system_dir_keys(mock_yaml_load, save_restore_system_dirs, tmp_path):
     assert folder_paths.get_user_directory() == os.path.normpath(str(tmp_path / "my_user"))
 
 
+@patch("yaml.safe_load")
+def test_system_dir_keys_not_applied_for_legacy(mock_yaml_load, save_restore_system_dirs, tmp_path):
+    """System directory keys are ignored when allow_system_dirs=False (legacy extra_model_paths.yaml)."""
+    original_output = folder_paths.get_output_directory()
+    config_data = {
+        "comfyui": {
+            "base_path": str(tmp_path),
+            "output": "my_output/",
+        }
+    }
+    mock_yaml_load.return_value = config_data
+
+    yaml_path = str(tmp_path / "extra_model_paths.yaml")
+    with open(yaml_path, "w") as f:
+        f.write("")
+
+    load_extra_path_config(yaml_path)  # allow_system_dirs defaults to False
+
+    # output should be unchanged — treated as a model category, not a system dir
+    assert folder_paths.get_output_directory() == original_output
+
+
 @patch("yaml.safe_load")
 def test_nested_models_block(mock_yaml_load, clear_folder_paths, tmp_path):
     """Nested models: block registers model paths relative to models/base_path."""
diff --git a/utils/extra_config.py b/utils/extra_config.py
index 1f957ad2b..8ba1bdc38 100644
--- a/utils/extra_config.py
+++ b/utils/extra_config.py
@@ -49,7 +49,7 @@ def _implicit_scan(base: str, exclude: set[str], is_default: bool) -> None:
             folder_paths.add_model_folder_path(category, path, is_default)
 
 
-def load_extra_path_config(yaml_path: str) -> None:
+def load_extra_path_config(yaml_path: str, allow_system_dirs: bool = False) -> None:
     with open(yaml_path, 'r', encoding='utf-8') as stream:
         config = yaml.safe_load(stream)
     yaml_dir = os.path.dirname(os.path.abspath(yaml_path))
@@ -68,7 +68,7 @@ def load_extra_path_config(yaml_path: str) -> None:
         flat_model_keys: set[str] = set()
 
         for key, value in conf.items():
-            if key in _SYSTEM_DIR_KEYS:
+            if allow_system_dirs and key in _SYSTEM_DIR_KEYS:
                 # System directory override → set_*_directory()
                 path = _resolve_base(str(value).strip(), block_base, yaml_dir)
                 logging.info("Setting %s directory to %s", key, path)