diff --git a/lib/galaxy/web/security/__init__.py b/lib/galaxy/web/security/__init__.py
index 29726ee6ea99..4a2ed331a97a 100644
--- a/lib/galaxy/web/security/__init__.py
+++ b/lib/galaxy/web/security/__init__.py
@@ -54,13 +54,13 @@ def encode_id( self, obj_id, kind=None ):
         # Encrypt
         return id_cipher.encrypt( s ).encode( 'hex' )
 
-    def encode_dict_ids( self, a_dict, kind=None ):
+    def encode_dict_ids( self, a_dict, kind=None, skip_startswith=None ):
         """
         Encode all ids in dictionary. Ids are identified by (a) an 'id' key or
         (b) a key that ends with '_id'
         """
         for key, val in a_dict.items():
-            if key == 'id' or key.endswith('_id'):
+            if key == 'id' or key.endswith('_id') and ( skip_startswith is None or not key.startswith( skip_startswith ) ):
                 a_dict[ key ] = self.encode_id( val, kind=kind )
 
         return a_dict
diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py
index 7ee0ab55fbcc..e3a7c168f54c 100644
--- a/lib/galaxy/webapps/galaxy/api/tools.py
+++ b/lib/galaxy/webapps/galaxy/api/tools.py
@@ -278,7 +278,7 @@ def create( self, trans, payload, **kwd ):
             # so it's possible to figure out which newly created elements
             # correspond with which tool file outputs
             output_dict[ 'output_name' ] = output_name
-            outputs.append( trans.security.encode_dict_ids( output_dict ) )
+            outputs.append( trans.security.encode_dict_ids( output_dict, skip_startswith="metadata_" ) )
 
         for job in vars.get('jobs', []):
             rval[ 'jobs' ].append( self.encode_all_ids( trans, job.to_dict( view='collection' ), recursive=True ) )