diff --git a/cmd/ctr/run.go b/cmd/ctr/run.go
index fb52ed45d..829e69c7a 100644
--- a/cmd/ctr/run.go
+++ b/cmd/ctr/run.go
@@ -111,7 +111,7 @@ var runCommand = cli.Command{
 			return err
 		}
 		if context.Bool("rm") {
-			defer container.Delete(ctx)
+			defer container.Delete(ctx, containerd.WithRootFSDeletion)
 		}
 		task, err := newTask(ctx, container, checkpointIndex, tty)
 		if err != nil {