diff --git a/src/org/exist/backup/Main.java b/src/org/exist/backup/Main.java
index 0db35ce3dde..0b4efc69218 100644
--- a/src/org/exist/backup/Main.java
+++ b/src/org/exist/backup/Main.java
@@ -377,7 +377,8 @@ private static void restoreWithoutGui(final String username, final String passwo
                     "as admin:\n\n" +
                     "import module namespace repair=\"http://exist-db.org/xquery/repo/repair\"\n" +
                     "at \"resource:org/exist/xquery/modules/expathrepo/repair.xql\";\n" +
-                    "repair:rebuild-all()\n");
+                    "repair:clean-all(),\n" +
+                    "repair:repair()\n");
         }
     }
     
diff --git a/src/org/exist/client/ClientFrame.java b/src/org/exist/client/ClientFrame.java
index bda97990635..aa06516ce50 100644
--- a/src/org/exist/client/ClientFrame.java
+++ b/src/org/exist/client/ClientFrame.java
@@ -1373,7 +1373,8 @@ public static void repairRepository(Collection collection) throws XMLDBException
         final XQueryService service = (XQueryService) collection.getService("XQueryService", "1.0");
         service.query("import module namespace repair=\"http://exist-db.org/xquery/repo/repair\"\n" +
                 "at \"resource:org/exist/xquery/modules/expathrepo/repair.xql\";\n" +
-                "repair:rebuild-all()");
+                "repair:clean-all(),\n" +
+                "repair:repair()");
     }
 
     public UserManagementService getUserManagementService() throws XMLDBException {