diff --git a/cli/cmd/cluster-apply.go b/cli/cmd/cluster-apply.go
index 0a75d1557..69f8debce 100644
--- a/cli/cmd/cluster-apply.go
+++ b/cli/cmd/cluster-apply.go
@@ -21,6 +21,7 @@ import (
 	log "github.com/sirupsen/logrus"
 	"github.com/spf13/cobra"
 
+	"github.com/kinvolk/lokomotive/internal"
 	"github.com/kinvolk/lokomotive/pkg/install"
 	"github.com/kinvolk/lokomotive/pkg/k8sutil"
 	"github.com/kinvolk/lokomotive/pkg/lokomotive"
@@ -84,6 +85,12 @@ func runClusterApply(cmd *cobra.Command, args []string) {
 		ctxLogger.Fatalf("Verify cluster: %v", err)
 	}
 
+	labels := map[string]string{}
+	internal.AppendNamespaceNameToLabels("kube-system", &labels)
+
+	if err := k8sutil.UpdateNamespaceWithLabels(labels, "kube-system", kubeconfigPath); err != nil {
+		ctxLogger.Fatalf("error updating namespace %q with labels: %q", "kube-system", err)
+	}
 	// Do controlplane upgrades only if cluster already exists and it is not a managed platform.
 	if exists && !p.Meta().Managed {
 		fmt.Printf("\nEnsuring that cluster controlplane is up to date.\n")
diff --git a/pkg/components/util/install.go b/pkg/components/util/install.go
index 95f69867f..2289f8617 100644
--- a/pkg/components/util/install.go
+++ b/pkg/components/util/install.go
@@ -62,6 +62,12 @@ func InstallComponent(c components.Component, kubeconfig string) error {
 		return fmt.Errorf("failed ensuring that namespace %q for component %q exists: %w", ns, name, err)
 	}
 
+	labels := c.GetNamespaceLabels()
+
+	if err := k8sutil.UpdateNamespaceWithLabels(labels, ns, kubeconfig); err != nil {
+		return fmt.Errorf("failed updating namespace %q with labels for component %q: %w", ns, name, err)
+	}
+
 	actionConfig, err := HelmActionConfig(ns, kubeconfig)
 	if err != nil {
 		return fmt.Errorf("failed preparing helm client: %w", err)