diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 08457df9aa2..bfad1c028cf 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -990,7 +990,7 @@ class JobWrapper(object, HasResourceParameters):
                 etype, evalue, tb = sys.exc_info()
 
             outputs_to_working_directory = util.asbool(self.get_destination_configuration("outputs_to_working_directory", False))
-            if outputs_to_working_directory:
+            if outputs_to_working_directory and not self.__link_file_check():
                 for dataset_path in self.get_output_fnames():
                     try:
                         shutil.move(dataset_path.false_path, dataset_path.real_path)