diff --git a/go/logic/applier.go b/go/logic/applier.go
index b7c33ad45..62fc5651e 100644
--- a/go/logic/applier.go
+++ b/go/logic/applier.go
@@ -988,6 +988,7 @@ func (this *Applier) AtomicCutOverMagicLock(sessionIdChan chan int64, tableLocke
 	}
 
 	defer func() {
+		query = fmt.Sprintf(`set /* gh-ost */ session wait_timeout:=%d`, this.migrationContext.ApplierWaitTimeout)
 		if _, err := sqlutils.ExecNoPrepare(this.db, query); err != nil {
 			this.migrationContext.Log.Errorf("Failed to restore applier wait_timeout to %d seconds: %v",
 				this.migrationContext.ApplierWaitTimeout, err,