diff --git a/controlplane/kubeadm/controllers/helpers.go b/controlplane/kubeadm/controllers/helpers.go
index e284754e6dc3..12e1b72d40ec 100644
--- a/controlplane/kubeadm/controllers/helpers.go
+++ b/controlplane/kubeadm/controllers/helpers.go
@@ -271,7 +271,7 @@ func (r *KubeadmControlPlaneReconciler) generateMachine(ctx context.Context, kcp
 			Name:        names.SimpleNameGenerator.GenerateName(kcp.Name + "-"),
 			Namespace:   kcp.Namespace,
 			Labels:      internal.ControlPlaneMachineLabelsForCluster(kcp, cluster.Name),
-			Annotations: kcp.Spec.MachineTemplate.ObjectMeta.Annotations,
+			Annotations: map[string]string{},
 			OwnerReferences: []metav1.OwnerReference{
 				*metav1.NewControllerRef(kcp, controlplanev1.GroupVersion.WithKind("KubeadmControlPlane")),
 			},
@@ -294,8 +294,11 @@ func (r *KubeadmControlPlaneReconciler) generateMachine(ctx context.Context, kcp
 	if err != nil {
 		return errors.Wrap(err, "failed to marshal cluster configuration")
 	}
-	if machine.Annotations == nil {
-		machine.Annotations = map[string]string{}
+
+	// Add the annotations from the MachineTemplate.
+	// Note: we intentionally don't use the map directly to ensure we don't modify the map in KCP.
+	for k, v := range kcp.Spec.MachineTemplate.ObjectMeta.Annotations {
+		machine.Annotations[k] = v
 	}
 	machine.Annotations[controlplanev1.KubeadmClusterConfigurationAnnotation] = string(clusterConfig)
 
diff --git a/controlplane/kubeadm/controllers/helpers_test.go b/controlplane/kubeadm/controllers/helpers_test.go
index b872d633dae6..2d02abc27827 100644
--- a/controlplane/kubeadm/controllers/helpers_test.go
+++ b/controlplane/kubeadm/controllers/helpers_test.go
@@ -486,6 +486,14 @@ func TestKubeadmControlPlaneReconciler_generateMachine(t *testing.T) {
 		},
 	}
 
+	kcpMachineTemplateObjectMeta := clusterv1.ObjectMeta{
+		Labels: map[string]string{
+			"machineTemplateLabel": "machineTemplateLabelValue",
+		},
+		Annotations: map[string]string{
+			"machineTemplateAnnotation": "machineTemplateAnnotationValue",
+		},
+	}
 	kcp := &controlplanev1.KubeadmControlPlane{
 		ObjectMeta: metav1.ObjectMeta{
 			Name:      "testControlPlane",
@@ -493,6 +501,9 @@ func TestKubeadmControlPlaneReconciler_generateMachine(t *testing.T) {
 		},
 		Spec: controlplanev1.KubeadmControlPlaneSpec{
 			Version: "v1.16.6",
+			MachineTemplate: controlplanev1.KubeadmControlPlaneMachineTemplate{
+				ObjectMeta: kcpMachineTemplateObjectMeta,
+			},
 		},
 	}
 
@@ -532,6 +543,19 @@ func TestKubeadmControlPlaneReconciler_generateMachine(t *testing.T) {
 	g.Expect(machine.OwnerReferences).To(HaveLen(1))
 	g.Expect(machine.OwnerReferences).To(ContainElement(*metav1.NewControllerRef(kcp, controlplanev1.GroupVersion.WithKind("KubeadmControlPlane"))))
 	g.Expect(machine.Spec).To(Equal(expectedMachineSpec))
+
+	// Verify that the machineTemplate.ObjectMeta has been propagated to the Machine.
+	for k, v := range kcpMachineTemplateObjectMeta.Labels {
+		g.Expect(machine.Labels[k]).To(Equal(v))
+	}
+	for k, v := range kcpMachineTemplateObjectMeta.Annotations {
+		g.Expect(machine.Annotations[k]).To(Equal(v))
+	}
+
+	// Verify that machineTemplate.ObjectMeta in KCP has not been modified.
+	g.Expect(kcp.Spec.MachineTemplate.ObjectMeta.Labels).NotTo(HaveKey(clusterv1.ClusterLabelName))
+	g.Expect(kcp.Spec.MachineTemplate.ObjectMeta.Labels).NotTo(HaveKey(clusterv1.MachineControlPlaneLabelName))
+	g.Expect(kcp.Spec.MachineTemplate.ObjectMeta.Annotations).NotTo(HaveKey(controlplanev1.KubeadmClusterConfigurationAnnotation))
 }
 
 func TestKubeadmControlPlaneReconciler_generateKubeadmConfig(t *testing.T) {
diff --git a/controlplane/kubeadm/internal/cluster_labels.go b/controlplane/kubeadm/internal/cluster_labels.go
index 4adffc6b948e..bb6be3a7472e 100644
--- a/controlplane/kubeadm/internal/cluster_labels.go
+++ b/controlplane/kubeadm/internal/cluster_labels.go
@@ -23,9 +23,12 @@ import (
 
 // ControlPlaneMachineLabelsForCluster returns a set of labels to add to a control plane machine for this specific cluster.
 func ControlPlaneMachineLabelsForCluster(kcp *controlplanev1.KubeadmControlPlane, clusterName string) map[string]string {
-	labels := kcp.Spec.MachineTemplate.ObjectMeta.Labels
-	if labels == nil {
-		labels = map[string]string{}
+	labels := map[string]string{}
+
+	// Add the labels from the MachineTemplate.
+	// Note: we intentionally don't use the map directly to ensure we don't modify the map in KCP.
+	for k, v := range kcp.Spec.MachineTemplate.ObjectMeta.Labels {
+		labels[k] = v
 	}
 
 	// Always force these labels over the ones coming from the spec.