diff --git a/kedro/config/omegaconf_config.py b/kedro/config/omegaconf_config.py
index 4d2ace59d4..37e92f211c 100644
--- a/kedro/config/omegaconf_config.py
+++ b/kedro/config/omegaconf_config.py
@@ -287,17 +287,20 @@ def load_and_merge_dir_config(  # noqa: too-many-arguments
             return {}
 
         if key == "parameters":
-            # Merge with runtime parameters only for "parameters"
-            return OmegaConf.to_container(
+            merged_conf = OmegaConf.to_container(
                 OmegaConf.merge(*aggregate_config, self.runtime_params), resolve=True
             )
-        return {
-            k: v
-            for k, v in OmegaConf.to_container(
-                OmegaConf.merge(*aggregate_config), resolve=True
-            ).items()
-            if not k.startswith("_")
-        }
+        else:
+            original_keys = OmegaConf.merge(*aggregate_config).keys()
+            merged_conf = {
+                k: v
+                for k, v in OmegaConf.to_container(
+                    OmegaConf.merge(*aggregate_config, self.runtime_params),
+                    resolve=True,
+                ).items()
+                if not k.startswith("_") and k in original_keys
+            }
+        return merged_conf
 
     def _is_valid_config_path(self, path):
         """Check if given path is a file path and file type is yaml or json."""