diff --git a/lib/galaxy/webapps/galaxy/services/tools.py b/lib/galaxy/webapps/galaxy/services/tools.py
index 2269a15efb22..853ce70925f0 100644
--- a/lib/galaxy/webapps/galaxy/services/tools.py
+++ b/lib/galaxy/webapps/galaxy/services/tools.py
@@ -270,6 +270,8 @@ def _handle_inputs_output_to_api_response(self, trans, tool, target_history, var
             output_dict["output_name"] = output_name
             outputs.append(output_dict)
 
+        trans.security.encode_all_ids(rval, recursive=True)
+
         for output_name, collection_instance in vars.get("output_collections", []):
             history = target_history or trans.history
             output_dict = dictify_dataset_collection_instance(
@@ -292,8 +294,6 @@ def _handle_inputs_output_to_api_response(self, trans, tool, target_history, var
             output_dict["output_name"] = output_name
             rval["implicit_collections"].append(output_dict)
 
-        trans.security.encode_all_ids(rval, recursive=True)
-
         # Encoding the job ids is handled by the pydantic model
         for job in vars.get("jobs", []):
             rval["jobs"].append(job.to_dict(view="collection"))