diff --git a/lib/galaxy/metadata/set_metadata.py b/lib/galaxy/metadata/set_metadata.py
index 1f381d91f09..e6a201d1999 100644
--- a/lib/galaxy/metadata/set_metadata.py
+++ b/lib/galaxy/metadata/set_metadata.py
@@ -42,6 +42,7 @@ from galaxy.model import (
     Dataset,
     HistoryDatasetAssociation,
     Job,
+    MetadataFile,
     store,
 )
 from galaxy.model.custom_types import total_size
@@ -420,6 +421,15 @@ def set_metadata_portable():
                     dataset.dataset.external_filename = None
                     dataset.dataset.extra_files_path = None
                 export_store.add_dataset(dataset)
+                for metadata in dataset.metadata.values():
+                    if isinstance(metadata, MetadataFile):
+                        object_store.update_from_file(
+                            metadata,
+                            file_name=metadata.file_name,
+                            extra_dir="_metadata_files",
+                            extra_dir_at_root=True,
+                            alt_name=os.path.basename(metadata.file_name),
+                        )
             else:
                 dataset.metadata.to_JSON_dict(filename_out)  # write out results of set_meta