diff --git a/lib/galaxy/web/controllers/root.py b/lib/galaxy/web/controllers/root.py
index 05a4ad5397e..f2b59c67b97 100644
--- a/lib/galaxy/web/controllers/root.py
+++ b/lib/galaxy/web/controllers/root.py
@@ -288,6 +288,7 @@ class RootController( BaseController ):
                     # Are *all* of the job's other output datasets deleted?
                     if job.check_if_output_datasets_deleted():
                         job.mark_deleted()                
+                        self.app.job_manager.job_stop_queue.put( job )
             self.app.model.flush()
 
     @web.expose