diff --git a/cmd/kubeadm/app/apis/kubeadm/validation/validation.go b/cmd/kubeadm/app/apis/kubeadm/validation/validation.go
index b40275107f0..c12795603e1 100644
--- a/cmd/kubeadm/app/apis/kubeadm/validation/validation.go
+++ b/cmd/kubeadm/app/apis/kubeadm/validation/validation.go
@@ -609,7 +609,9 @@ func isAllowedFlag(flagName string) bool {
 		kubeadmcmdoptions.NodeName,
 		kubeadmcmdoptions.KubeconfigDir,
 		kubeadmcmdoptions.UploadCerts,
+		kubeadmcmdoptions.FeatureGatesString,                                       // TODO: remove this line when --feature-gates flag is deprecated and dropped from "kubeadm upgrade apply/plan"
 		"api-server-manifest", "controller-manager-manifest", "scheduler-manifest", // TODO: remove this line when these flags are deprecated and dropped from "kubeadm upgrade diff"
+		"allow-missing-template-keys", "output", "show-managed-fields",
 		"print-join-command", "rootfs", "v", "log-file", "yes")
 	if allowedFlags.Has(flagName) {
 		return true
diff --git a/cmd/kubeadm/app/cmd/upgrade/common.go b/cmd/kubeadm/app/cmd/upgrade/common.go
index d01a26710f1..2f339676619 100644
--- a/cmd/kubeadm/app/cmd/upgrade/common.go
+++ b/cmd/kubeadm/app/cmd/upgrade/common.go
@@ -143,14 +143,6 @@ func enforceRequirements(flagSet *pflag.FlagSet, flags *applyPlanFlags, args []s
 		return nil, nil, nil, nil, errors.Wrap(err, "[upgrade/health] FATAL")
 	}
 
-	// If features gates are passed to the command line, use it (otherwise use featureGates from configuration)
-	if flags.featureGatesString != "" {
-		initCfg.FeatureGates, err = features.NewFeatureGate(&features.InitFeatureGates, flags.featureGatesString)
-		if err != nil {
-			return nil, nil, nil, nil, errors.Wrap(err, "[upgrade/config] FATAL")
-		}
-	}
-
 	// Check if feature gate flags used in the cluster are consistent with the set of features currently supported by kubeadm
 	if msg := features.CheckDeprecatedFlags(&features.InitFeatureGates, initCfg.FeatureGates); len(msg) > 0 {
 		for _, m := range msg {
diff --git a/cmd/kubeadm/app/cmd/upgrade/upgrade.go b/cmd/kubeadm/app/cmd/upgrade/upgrade.go
index 902e2cbccb9..1145196557c 100644
--- a/cmd/kubeadm/app/cmd/upgrade/upgrade.go
+++ b/cmd/kubeadm/app/cmd/upgrade/upgrade.go
@@ -17,11 +17,13 @@ limitations under the License.
 package upgrade
 
 import (
+	"fmt"
 	"io"
 
 	"github.com/spf13/cobra"
 	"github.com/spf13/pflag"
 
+	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/kubernetes/cmd/kubeadm/app/cmd/options"
 	cmdutil "k8s.io/kubernetes/cmd/kubeadm/app/cmd/util"
 	kubeadmconstants "k8s.io/kubernetes/cmd/kubeadm/app/constants"
@@ -71,6 +73,8 @@ func addApplyPlanFlags(fs *pflag.FlagSet, flags *applyPlanFlags) {
 	fs.BoolVar(&flags.allowExperimentalUpgrades, "allow-experimental-upgrades", flags.allowExperimentalUpgrades, "Show unstable versions of Kubernetes as an upgrade alternative and allow upgrading to an alpha/beta/release candidate versions of Kubernetes.")
 	fs.BoolVar(&flags.allowRCUpgrades, "allow-release-candidate-upgrades", flags.allowRCUpgrades, "Show release candidate versions of Kubernetes as an upgrade alternative and allow upgrading to a release candidate versions of Kubernetes.")
 	fs.BoolVar(&flags.printConfig, "print-config", flags.printConfig, "Specifies whether the configuration file that will be used in the upgrade should be printed or not.")
-	options.AddFeatureGatesStringFlag(fs, &flags.featureGatesString)
+	options.AddFeatureGatesStringFlag(fs, &flags.featureGatesString) // TODO: remove in 1.32
+	_ = fs.MarkDeprecated(options.FeatureGatesString, fmt.Sprintf("This flag is deprecated and no-op now. It will be removed in a future release. The upgrade workflow is not designed to reconfigure the cluster. "+
+		"Please edit the 'featureGates' field of ClusterConfiguration which is defined in the %s/%s ConfigMap instead.", metav1.NamespaceSystem, kubeadmconstants.KubeadmConfigConfigMap))
 	options.AddIgnorePreflightErrorsFlag(fs, &flags.ignorePreflightErrors)
 }