diff --git a/cmd/kubeadm/app/apis/kubeadm/validation/validation.go b/cmd/kubeadm/app/apis/kubeadm/validation/validation.go
index fb92ea1aea1..b40275107f0 100644
--- a/cmd/kubeadm/app/apis/kubeadm/validation/validation.go
+++ b/cmd/kubeadm/app/apis/kubeadm/validation/validation.go
@@ -609,6 +609,7 @@ func isAllowedFlag(flagName string) bool {
 		kubeadmcmdoptions.NodeName,
 		kubeadmcmdoptions.KubeconfigDir,
 		kubeadmcmdoptions.UploadCerts,
+		"api-server-manifest", "controller-manager-manifest", "scheduler-manifest", // TODO: remove this line when these flags are deprecated and dropped from "kubeadm upgrade diff"
 		"print-join-command", "rootfs", "v", "log-file", "yes")
 	if allowedFlags.Has(flagName) {
 		return true
diff --git a/cmd/kubeadm/app/cmd/upgrade/diff.go b/cmd/kubeadm/app/cmd/upgrade/diff.go
index bd5a1f52983..5f5c42d93c3 100644
--- a/cmd/kubeadm/app/cmd/upgrade/diff.go
+++ b/cmd/kubeadm/app/cmd/upgrade/diff.go
@@ -89,8 +89,11 @@ func newCmdDiff(out io.Writer) *cobra.Command {
 	options.AddKubeConfigFlag(cmd.Flags(), &flags.kubeConfigPath)
 	options.AddConfigFlag(cmd.Flags(), &flags.cfgPath)
 	cmd.Flags().StringVar(&flags.apiServerManifestPath, "api-server-manifest", defaultAPIServerManifestPath, "path to API server manifest")
+	cmd.Flags().MarkDeprecated("api-server-manifest", "This flag is deprecated and will be removed in a future release.")
 	cmd.Flags().StringVar(&flags.controllerManagerManifestPath, "controller-manager-manifest", defaultControllerManagerManifestPath, "path to controller manifest")
+	cmd.Flags().MarkDeprecated("controller-manager-manifest", "This flag is deprecated and will be removed in a future release.")
 	cmd.Flags().StringVar(&flags.schedulerManifestPath, "scheduler-manifest", defaultSchedulerManifestPath, "path to scheduler manifest")
+	cmd.Flags().MarkDeprecated("scheduler-manifest", "This flag is deprecated and will be removed in a future release.")
 	cmd.Flags().IntVarP(&flags.contextLines, "context-lines", "c", 3, "How many lines of context in the diff")
 
 	return cmd