diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index d0911bbc056c..c2c062d2ae9c 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1752,9 +1752,14 @@ def setup_external_metadata(self, exec_dir=None, tmp_dir=None,
         if datatypes_config is None:
             datatypes_config = os.path.join(self.working_directory, 'registry.xml')
             self.app.datatypes_registry.to_xml_file(path=datatypes_config)
-        command = self.external_output_metadata.setup_external_metadata([output_dataset_assoc.dataset for
-                                                                         output_dataset_assoc in
-                                                                         job.output_datasets + job.output_library_datasets],
+
+        output_datasets = {}
+        for output_dataset_assoc in job.output_datasets + job.output_library_datasets:
+            output_name = output_dataset_assoc.name
+            assert output_name not in output_datasets
+            output_datasets[output_dataset_assoc.name] = output_dataset_assoc.dataset
+
+        command = self.external_output_metadata.setup_external_metadata(output_datasets,
                                                                         self.sa_session,
                                                                         exec_dir=exec_dir,
                                                                         tmp_dir=tmp_dir,
diff --git a/lib/galaxy/metadata/__init__.py b/lib/galaxy/metadata/__init__.py
index ebfca7994782..2c4fcfcda181 100644
--- a/lib/galaxy/metadata/__init__.py
+++ b/lib/galaxy/metadata/__init__.py
@@ -38,7 +38,7 @@ def cleanup_external_metadata(self, sa_session):
         pass
 
     @abc.abstractmethod
-    def setup_external_metadata(self, datasets, sa_session, exec_dir=None,
+    def setup_external_metadata(self, datasets_dict, sa_session, exec_dir=None,
                                 tmp_dir=None, dataset_files_path=None,
                                 output_fnames=None, config_root=None,
                                 config_file=None, datatypes_config=None,
@@ -104,7 +104,7 @@ def invalidate_external_metadata(self, datasets, sa_session):
                 sa_session.flush()
                 jeom = self._get_output_filenames_by_dataset(dataset, sa_session)
 
-    def setup_external_metadata(self, datasets, sa_session, exec_dir=None,
+    def setup_external_metadata(self, datasets_dict, sa_session, exec_dir=None,
                                 tmp_dir=None, dataset_files_path=None,
                                 output_fnames=None, config_root=None,
                                 config_file=None, datatypes_config=None,
@@ -143,8 +143,8 @@ def __get_filename_override():
                 metadata_path_on_compute(metadata_files.filename_override_metadata),
             )
             return line
-        if not isinstance(datasets, list):
-            datasets = [datasets]
+
+        datasets = list(datasets_dict.values())
         if exec_dir is None:
             exec_dir = os.path.abspath(os.getcwd())
         if dataset_files_path is None:
diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py
index 9038a7f2fb6d..2b0afc46dec1 100644
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -75,7 +75,10 @@ def execute_via_app(self, tool, app, session_id, history_id, user=None,
         datatypes_config = os.path.join(job_working_dir, 'registry.xml')
         app.datatypes_registry.to_xml_file(path=datatypes_config)
         external_metadata_wrapper = get_metadata_compute_strategy(app, job.id)
-        cmd_line = external_metadata_wrapper.setup_external_metadata(dataset,
+        output_datatasets_dict = {
+            dataset_name: dataset,
+        }
+        cmd_line = external_metadata_wrapper.setup_external_metadata(output_datatasets_dict,
                                                                      sa_session,
                                                                      exec_dir=None,
                                                                      tmp_dir=job_working_dir,