diff --git a/internal/controllers/topology/cluster/reconcile_state.go b/internal/controllers/topology/cluster/reconcile_state.go
index 9c1accce86f0..c6fa0090df73 100644
--- a/internal/controllers/topology/cluster/reconcile_state.go
+++ b/internal/controllers/topology/cluster/reconcile_state.go
@@ -464,7 +464,7 @@ func (r *Reconciler) reconcileMachineHealthCheck(ctx context.Context, current, d
 		if err != nil {
 			return errors.Wrapf(err, "failed to create patch helper for MachineHealthCheck %s", klog.KObj(desired))
 		}
-		if err := helper.Patch(ctx); err != nil {
+		if _, err := helper.Patch(ctx); err != nil {
 			return errors.Wrapf(err, "failed to create MachineHealthCheck %s", klog.KObj(desired))
 		}
 		r.recorder.Eventf(desired, corev1.EventTypeNormal, createEventReason, "Created MachineHealthCheck %q", klog.KObj(desired))
@@ -500,7 +500,7 @@ func (r *Reconciler) reconcileMachineHealthCheck(ctx context.Context, current, d
 	}
 
 	log.Info("Patching MachineHealthCheck")
-	if err := patchHelper.Patch(ctx); err != nil {
+	if _, err := patchHelper.Patch(ctx); err != nil {
 		return errors.Wrapf(err, "failed to patch MachineHealthCheck %s", klog.KObj(current))
 	}
 	r.recorder.Eventf(current, corev1.EventTypeNormal, updateEventReason, "Updated MachineHealthCheck %q", klog.KObj(current))
@@ -530,7 +530,8 @@ func (r *Reconciler) reconcileCluster(ctx context.Context, s *scope.Scope) error
 	} else {
 		log.Info("Patching Cluster", "diff", string(changes))
 	}
-	if err := patchHelper.Patch(ctx); err != nil {
+	modifiedResourceVersion, err := patchHelper.Patch(ctx)
+	if err != nil {
 		return errors.Wrapf(err, "failed to patch Cluster %s", klog.KObj(s.Current.Cluster))
 	}
 	r.recorder.Eventf(s.Current.Cluster, corev1.EventTypeNormal, updateEventReason, "Updated Cluster %q", klog.KObj(s.Current.Cluster))
@@ -538,11 +539,10 @@ func (r *Reconciler) reconcileCluster(ctx context.Context, s *scope.Scope) error
 	// Wait until Cluster is updated in the cache.
 	// Note: We have to do this because otherwise using a cached client in the Reconcile func could
 	// return a stale state of the Cluster we just patched (because the cache might be stale).
-	// Note: It is good enough to check that the resource version changed. Other controllers might have updated the
-	// Cluster as well, but the combination of the patch call above without a conflict and a changed resource
-	// version here guarantees that we see the changes of our own update.
 	// Note: Using DeepCopy to not modify s.Current.Cluster as it's not trivial to figure out what impact that would have.
-	return clientutil.WaitForCacheToBeUpToDate(ctx, r.Client, "Cluster update", s.Current.Cluster.DeepCopy())
+	cluster := s.Current.Cluster.DeepCopy()
+	cluster.ResourceVersion = modifiedResourceVersion
+	return clientutil.WaitForCacheToBeUpToDate(ctx, r.Client, "Cluster update", cluster)
 }
 
 // reconcileMachineDeployments reconciles the desired state of the MachineDeployment objects.
@@ -693,7 +693,7 @@ func (r *Reconciler) createMachineDeployment(ctx context.Context, s *scope.Scope
 		bootstrapCleanupFunc()
 		return createErrorWithoutObjectName(ctx, err, md.Object)
 	}
-	if err := helper.Patch(ctx); err != nil {
+	if _, err := helper.Patch(ctx); err != nil {
 		// Best effort cleanup of the InfrastructureMachineTemplate & BootstrapTemplate (only on creation).
 		infrastructureMachineCleanupFunc()
 		bootstrapCleanupFunc()
@@ -814,7 +814,8 @@ func (r *Reconciler) updateMachineDeployment(ctx context.Context, s *scope.Scope
 	} else {
 		log.Info("Patching MachineDeployment", "diff", string(changes))
 	}
-	if err := patchHelper.Patch(ctx); err != nil {
+	modifiedResourceVersion, err := patchHelper.Patch(ctx)
+	if err != nil {
 		// Best effort cleanup of the InfrastructureMachineTemplate & BootstrapTemplate (only on template rotation).
 		infrastructureMachineCleanupFunc()
 		bootstrapCleanupFunc()
@@ -825,10 +826,10 @@ func (r *Reconciler) updateMachineDeployment(ctx context.Context, s *scope.Scope
 	// Wait until MachineDeployment is updated in the cache.
 	// Note: We have to do this because otherwise using a cached client in current state could
 	// return a stale state of a MachineDeployment we just patched (because the cache might be stale).
-	// Note: It is good enough to check that the resource version changed. Other controllers might have updated the
-	// MachineDeployment as well, but the combination of the patch call above without a conflict and a changed resource
-	// version here guarantees that we see the changes of our own update.
-	if err := clientutil.WaitForCacheToBeUpToDate(ctx, r.Client, "MachineDeployment update", currentMD.Object); err != nil {
+	// Note: Using DeepCopy to not modify currentMD.Object as it's not trivial to figure out what impact that would have.
+	md := currentMD.Object.DeepCopy()
+	md.ResourceVersion = modifiedResourceVersion
+	if err := clientutil.WaitForCacheToBeUpToDate(ctx, r.Client, "MachineDeployment update", md); err != nil {
 		return err
 	}
 
@@ -1016,7 +1017,7 @@ func (r *Reconciler) createMachinePool(ctx context.Context, s *scope.Scope, mp *
 		bootstrapCleanupFunc()
 		return createErrorWithoutObjectName(ctx, err, mp.Object)
 	}
-	if err := helper.Patch(ctx); err != nil {
+	if _, err := helper.Patch(ctx); err != nil {
 		// Best effort cleanup of the InfrastructureMachinePool & BootstrapConfig (only on creation).
 		infrastructureMachineMachinePoolCleanupFunc()
 		bootstrapCleanupFunc()
@@ -1077,7 +1078,8 @@ func (r *Reconciler) updateMachinePool(ctx context.Context, s *scope.Scope, mpTo
 	} else {
 		log.Info("Patching MachinePool", "diff", string(changes))
 	}
-	if err := patchHelper.Patch(ctx); err != nil {
+	modifiedResourceVersion, err := patchHelper.Patch(ctx)
+	if err != nil {
 		return errors.Wrapf(err, "failed to patch MachinePool %s", klog.KObj(currentMP.Object))
 	}
 	r.recorder.Eventf(cluster, corev1.EventTypeNormal, updateEventReason, "Updated MachinePool %q%s", klog.KObj(currentMP.Object), logMachinePoolVersionChange(currentMP.Object, desiredMP.Object))
@@ -1088,7 +1090,9 @@ func (r *Reconciler) updateMachinePool(ctx context.Context, s *scope.Scope, mpTo
 	// Note: It is good enough to check that the resource version changed. Other controllers might have updated the
 	// MachinePool as well, but the combination of the patch call above without a conflict and a changed resource
 	// version here guarantees that we see the changes of our own update.
-	if err := clientutil.WaitForCacheToBeUpToDate(ctx, r.Client, "MachinePool update", currentMP.Object); err != nil {
+	mp := currentMP.Object.DeepCopy()
+	mp.ResourceVersion = modifiedResourceVersion
+	if err := clientutil.WaitForCacheToBeUpToDate(ctx, r.Client, "MachinePool update", mp); err != nil {
 		return err
 	}
 
@@ -1193,7 +1197,7 @@ func (r *Reconciler) reconcileReferencedObject(ctx context.Context, in reconcile
 		if err != nil {
 			return false, errors.Wrap(createErrorWithoutObjectName(ctx, err, in.desired), "failed to create patch helper")
 		}
-		if err := helper.Patch(ctx); err != nil {
+		if _, err := helper.Patch(ctx); err != nil {
 			return false, createErrorWithoutObjectName(ctx, err, in.desired)
 		}
 		r.recorder.Eventf(in.cluster, corev1.EventTypeNormal, createEventReason, "Created %s %q", in.desired.GetKind(), klog.KObj(in.desired))
@@ -1224,7 +1228,7 @@ func (r *Reconciler) reconcileReferencedObject(ctx context.Context, in reconcile
 	} else {
 		log.Info(fmt.Sprintf("Patching %s", in.desired.GetKind()), "diff", string(changes))
 	}
-	if err := patchHelper.Patch(ctx); err != nil {
+	if _, err := patchHelper.Patch(ctx); err != nil {
 		return false, errors.Wrapf(err, "failed to patch %s %s", in.current.GetKind(), klog.KObj(in.current))
 	}
 	r.recorder.Eventf(in.cluster, corev1.EventTypeNormal, updateEventReason, "Updated %s %q%s", in.desired.GetKind(), klog.KObj(in.desired), logUnstructuredVersionChange(in.current, in.desired, in.versionGetter))
@@ -1279,7 +1283,7 @@ func (r *Reconciler) reconcileReferencedTemplate(ctx context.Context, in reconci
 		if err != nil {
 			return false, errors.Wrap(createErrorWithoutObjectName(ctx, err, in.desired), "failed to create patch helper")
 		}
-		if err := helper.Patch(ctx); err != nil {
+		if _, err := helper.Patch(ctx); err != nil {
 			return false, createErrorWithoutObjectName(ctx, err, in.desired)
 		}
 		r.recorder.Eventf(in.cluster, corev1.EventTypeNormal, createEventReason, "Created %s %q", in.desired.GetKind(), klog.KObj(in.desired))
@@ -1319,7 +1323,7 @@ func (r *Reconciler) reconcileReferencedTemplate(ctx context.Context, in reconci
 		} else {
 			log.Info(fmt.Sprintf("Patching %s", in.desired.GetKind()), "diff", string(changes))
 		}
-		if err := patchHelper.Patch(ctx); err != nil {
+		if _, err := patchHelper.Patch(ctx); err != nil {
 			return false, errors.Wrapf(err, "failed to patch %s %s", in.desired.GetKind(), klog.KObj(in.desired))
 		}
 		r.recorder.Eventf(in.cluster, corev1.EventTypeNormal, updateEventReason, "Updated %s %q (metadata changes)", in.desired.GetKind(), klog.KObj(in.desired))
@@ -1344,7 +1348,7 @@ func (r *Reconciler) reconcileReferencedTemplate(ctx context.Context, in reconci
 	if err != nil {
 		return false, errors.Wrap(createErrorWithoutObjectName(ctx, err, in.desired), "failed to create patch helper")
 	}
-	if err := helper.Patch(ctx); err != nil {
+	if _, err := helper.Patch(ctx); err != nil {
 		return false, createErrorWithoutObjectName(ctx, err, in.desired)
 	}
 	r.recorder.Eventf(in.cluster, corev1.EventTypeNormal, createEventReason, "Created %s %q as a replacement for %q (template rotation)", in.desired.GetKind(), klog.KObj(in.desired), in.ref.Name)
diff --git a/internal/controllers/topology/cluster/structuredmerge/interfaces.go b/internal/controllers/topology/cluster/structuredmerge/interfaces.go
index 2842ca4e7be7..61e99c81dc70 100644
--- a/internal/controllers/topology/cluster/structuredmerge/interfaces.go
+++ b/internal/controllers/topology/cluster/structuredmerge/interfaces.go
@@ -41,5 +41,5 @@ type PatchHelper interface {
 	Changes() []byte
 
 	// Patch patches the given obj in the Kubernetes cluster.
-	Patch(ctx context.Context) error
+	Patch(ctx context.Context) (modifiedResourceVersion string, err error)
 }
diff --git a/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper.go b/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper.go
index 2e029c966d73..475a258aa8cd 100644
--- a/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper.go
+++ b/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper.go
@@ -133,9 +133,9 @@ func (h *serverSidePatchHelper) HasChanges() bool {
 }
 
 // Patch will server side apply the current intent (the modified object.
-func (h *serverSidePatchHelper) Patch(ctx context.Context) error {
+func (h *serverSidePatchHelper) Patch(ctx context.Context) (string, error) {
 	if !h.HasChanges() {
-		return nil
+		return "", nil
 	}
 
 	log := ctrl.LoggerFrom(ctx)
@@ -147,5 +147,8 @@ func (h *serverSidePatchHelper) Patch(ctx context.Context) error {
 		// overwrite values and become sole manager.
 		client.ForceOwnership,
 	}
-	return h.client.Apply(ctx, client.ApplyConfigurationFromUnstructured(h.modified), options...)
+	if err := h.client.Apply(ctx, client.ApplyConfigurationFromUnstructured(h.modified), options...); err != nil {
+		return "", err
+	}
+	return h.modified.GetResourceVersion(), nil
 }
diff --git a/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper_test.go b/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper_test.go
index 47d10335afc3..85c661abd465 100644
--- a/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper_test.go
+++ b/internal/controllers/topology/cluster/structuredmerge/serversidepathhelper_test.go
@@ -104,7 +104,8 @@ func TestServerSideApply(t *testing.T) {
 		g.Expect(p0.Changes()).To(BeNil()) // changes are expected to be nil on create.
 
 		// Create the object using server side apply
-		g.Expect(p0.Patch(ctx)).To(Succeed())
+		_, err = p0.Patch(ctx)
+		g.Expect(err).ToNot(HaveOccurred())
 
 		// Check the object and verify managed field are properly set.
 		got := obj.DeepCopy()
@@ -306,7 +307,8 @@ func TestServerSideApply(t *testing.T) {
 		g.Expect(p0.Changes()).To(BeNil())
 
 		// Change the object using server side apply
-		g.Expect(p0.Patch(ctx)).To(Succeed())
+		_, err = p0.Patch(ctx)
+		g.Expect(err).ToNot(HaveOccurred())
 
 		// Check the object and verify fields set by the other controller are preserved.
 		got := obj.DeepCopy()
@@ -354,7 +356,8 @@ func TestServerSideApply(t *testing.T) {
 		g.Expect(p0.Changes()).To(Equal([]byte(`{"spec":{"controlPlaneEndpoint":{"host":"changed"}}}`)))
 
 		// Create the object using server side apply
-		g.Expect(p0.Patch(ctx)).To(Succeed())
+		_, err = p0.Patch(ctx)
+		g.Expect(err).ToNot(HaveOccurred())
 
 		// Check the object and verify the change is applied as well as the fields set by the other controller are still preserved.
 		got := obj.DeepCopy()
@@ -393,7 +396,8 @@ func TestServerSideApply(t *testing.T) {
 		g.Expect(p0.Changes()).To(BeEmpty()) // Note: metadata.managedFields have been removed from the diff to reduce log verbosity.
 
 		// Create the object using server side apply
-		g.Expect(p0.Patch(ctx)).To(Succeed())
+		_, err = p0.Patch(ctx)
+		g.Expect(err).ToNot(HaveOccurred())
 
 		// Check the object and verify the change is applied as well as managed field updated accordingly.
 		got := obj.DeepCopy()
@@ -434,7 +438,8 @@ func TestServerSideApply(t *testing.T) {
 		g.Expect(p0.Changes()).To(Equal([]byte(`{"spec":{"bar":"changed-by-topology-controller"}}`)))
 
 		// Create the object using server side apply
-		g.Expect(p0.Patch(ctx)).To(Succeed())
+		_, err = p0.Patch(ctx)
+		g.Expect(err).ToNot(HaveOccurred())
 
 		// Check the object and verify the change is applied as well as managed field updated accordingly.
 		got := obj.DeepCopy()
@@ -667,7 +672,8 @@ func TestServerSideApplyWithDefaulting(t *testing.T) {
 			g.Expect(err).ToNot(HaveOccurred())
 			g.Expect(p0.HasChanges()).To(BeTrue())
 			g.Expect(p0.HasSpecChanges()).To(BeTrue())
-			g.Expect(p0.Patch(ctx)).To(Succeed())
+			_, err = p0.Patch(ctx)
+			g.Expect(err).ToNot(HaveOccurred())
 			defer func() {
 				g.Expect(env.CleanupAndWait(ctx, kct.DeepCopy())).To(Succeed())
 			}()
@@ -731,7 +737,8 @@ func TestServerSideApplyWithDefaulting(t *testing.T) {
 			g.Expect(err).ToNot(HaveOccurred())
 			g.Expect(p0.HasChanges()).To(Equal(tt.expectChanges), fmt.Sprintf("changes: %s", string(p0.Changes())))
 			g.Expect(p0.HasSpecChanges()).To(Equal(tt.expectSpecChanges))
-			g.Expect(p0.Patch(ctx)).To(Succeed())
+			_, err = p0.Patch(ctx)
+			g.Expect(err).ToNot(HaveOccurred())
 
 			// Verify field ownership
 			// Note: It might take a bit for the cache to be up-to-date.
@@ -779,7 +786,8 @@ func TestServerSideApplyWithDefaulting(t *testing.T) {
 				// Expect no changes.
 				g.Expect(p0.HasChanges()).To(BeFalse())
 				g.Expect(p0.HasSpecChanges()).To(BeFalse())
-				g.Expect(p0.Patch(ctx)).To(Succeed())
+				_, err := p0.Patch(ctx)
+				g.Expect(err).ToNot(HaveOccurred())
 
 				// Expect webhook to be called.
 				g.Expect(defaulter.Counter).To(Equal(countBefore+2),
@@ -806,7 +814,8 @@ func TestServerSideApplyWithDefaulting(t *testing.T) {
 			// Expect no changes.
 			g.Expect(p0.HasChanges()).To(BeFalse())
 			g.Expect(p0.HasSpecChanges()).To(BeFalse())
-			g.Expect(p0.Patch(ctx)).To(Succeed())
+			_, err = p0.Patch(ctx)
+			g.Expect(err).ToNot(HaveOccurred())
 
 			// Expect webhook to not be called.
 			g.Expect(defaulter.Counter).To(Equal(countBefore),