diff --git a/spacy/tests/serialize/test_serialize_config.py b/spacy/tests/serialize/test_serialize_config.py
index 85e6f8b2c..7d96c9063 100644
--- a/spacy/tests/serialize/test_serialize_config.py
+++ b/spacy/tests/serialize/test_serialize_config.py
@@ -415,6 +415,27 @@ def test_config_overrides():
     assert nlp.pipe_names == ["tok2vec", "tagger"]
 
 
+def test_config_overrides_registered_functions():
+    nlp = spacy.blank("en")
+    nlp.add_pipe("attribute_ruler")
+    with make_tempdir() as d:
+        nlp.to_disk(d)
+        nlp = spacy.load(
+            d,
+            config={
+                "components": {
+                    "attribute_ruler": {
+                        "scorer": {"@scorers": "spacy.tagger_scorer.v1"}
+                    }
+                }
+            },
+        )
+        assert (
+            nlp.config["components"]["attribute_ruler"]["scorer"]["@scorers"]
+            == "spacy.tagger_scorer.v1"
+        )
+
+
 def test_config_interpolation():
     config = Config().from_str(nlp_config_string, interpolate=False)
     assert config["corpora"]["train"]["path"] == "${paths.train}"
diff --git a/spacy/util.py b/spacy/util.py
index 8cc89217d..ac38fbc90 100644
--- a/spacy/util.py
+++ b/spacy/util.py
@@ -1530,10 +1530,14 @@ def set_dot_to_object(config: Config, section: str, value: Any) -> None:
 def walk_dict(
     node: Dict[str, Any], parent: List[str] = []
 ) -> Iterator[Tuple[List[str], Any]]:
-    """Walk a dict and yield the path and values of the leaves."""
+    """Walk a dict and yield the path and values of the leaves, treating
+    registered functions that start with @ as final values rather than dicts to
+    traverse."""
     for key, value in node.items():
         key_parent = [*parent, key]
-        if isinstance(value, dict):
+        if isinstance(value, dict) and not any(
+            value_key.startswith("@") for value_key in value
+        ):
             yield from walk_dict(value, key_parent)
         else:
             yield (key_parent, value)