diff --git a/cmd/kubeadm/app/cmd/phases/init/certs.go b/cmd/kubeadm/app/cmd/phases/init/certs.go
index c7ea16044d3..4338ba5d40e 100644
--- a/cmd/kubeadm/app/cmd/phases/init/certs.go
+++ b/cmd/kubeadm/app/cmd/phases/init/certs.go
@@ -66,7 +66,9 @@ func NewCertsPhase() workflow.Phase {
 func localFlags() *pflag.FlagSet {
 	set := pflag.NewFlagSet("csr", pflag.ExitOnError)
 	options.AddCSRFlag(set, &csrOnly)
+	set.MarkDeprecated(options.CSROnly, "This flag will be removed in a future version. Please use kubeadm alpha certs generate-csr instead.")
 	options.AddCSRDirFlag(set, &csrDir)
+	set.MarkDeprecated(options.CSRDir, "This flag will be removed in a future version. Please use kubeadm alpha certs generate-csr instead.")
 	return set
 }