diff --git a/pkg/canary/util.go b/pkg/canary/util.go
index e7deb6c07..8ebc06154 100644
--- a/pkg/canary/util.go
+++ b/pkg/canary/util.go
@@ -83,6 +83,10 @@ func makeAnnotations(annotations map[string]string) (map[string]string, error) {
 	id := fmt.Sprintf("%x-%x-%x-%x-%x", uuid[0:4], uuid[4:6], uuid[6:8], uuid[8:10], uuid[10:])
 
 	for k, v := range annotations {
+		// skip Flux GC markers
+		if strings.Contains(k, "/checksum") {
+			continue
+		}
 		if k != idKey {
 			res[k] = v
 		}
diff --git a/pkg/router/ingress.go b/pkg/router/ingress.go
index 01fd58a3a..2f605d8bb 100644
--- a/pkg/router/ingress.go
+++ b/pkg/router/ingress.go
@@ -211,7 +211,7 @@ func (i *IngressRouter) SetRoutes(
 
 func (i *IngressRouter) makeAnnotations(annotations map[string]string) map[string]string {
 	res := make(map[string]string)
-	for k, v := range annotations {
+	for k, v := range makeAnnotations(annotations) {
 		if !strings.Contains(k, i.GetAnnotationWithPrefix("canary")) &&
 			!strings.Contains(k, "kubectl.kubernetes.io/last-applied-configuration") &&
 			!strings.Contains(k, i.GetAnnotationWithPrefix("canary-weight")) &&
@@ -232,7 +232,7 @@ func (i *IngressRouter) makeAnnotations(annotations map[string]string) map[strin
 func (i *IngressRouter) makeHeaderAnnotations(annotations map[string]string,
 	header string, headerValue string, headerRegex string, cookie string) map[string]string {
 	res := make(map[string]string)
-	for k, v := range annotations {
+	for k, v := range makeAnnotations(annotations) {
 		if !strings.Contains(v, i.GetAnnotationWithPrefix("canary")) {
 			res[k] = v
 		}
diff --git a/pkg/router/istio.go b/pkg/router/istio.go
index 7cf6d6f18..6794b28ab 100644
--- a/pkg/router/istio.go
+++ b/pkg/router/istio.go
@@ -259,6 +259,8 @@ func (ir *IstioRouter) reconcileVirtualService(canary *flaggerv1.Canary) error {
 
 				if vtClone.ObjectMeta.Annotations == nil {
 					vtClone.ObjectMeta.Annotations = make(map[string]string)
+				} else {
+					vtClone.ObjectMeta.Annotations = makeAnnotations(vtClone.ObjectMeta.Annotations)
 				}
 
 				vtClone.ObjectMeta.Annotations[configAnnotation] = string(b)
diff --git a/pkg/router/kubernetes_default.go b/pkg/router/kubernetes_default.go
index a289ae3a6..3f79bf2bc 100644
--- a/pkg/router/kubernetes_default.go
+++ b/pkg/router/kubernetes_default.go
@@ -206,8 +206,8 @@ func (c *KubernetesDefaultRouter) reconcileService(canary *flaggerv1.Canary, nam
 			if svc.ObjectMeta.Annotations == nil {
 				svc.ObjectMeta.Annotations = make(map[string]string)
 			}
-			if diff := cmp.Diff(metadata.Annotations, svc.ObjectMeta.Annotations); diff != "" {
-				svcClone.ObjectMeta.Annotations = metadata.Annotations
+			if diff := cmp.Diff(makeAnnotations(metadata.Annotations), svc.ObjectMeta.Annotations); diff != "" {
+				svcClone.ObjectMeta.Annotations = makeAnnotations(metadata.Annotations)
 				updateService = true
 			}
 			if diff := cmp.Diff(metadata.Labels, svc.ObjectMeta.Labels); diff != "" {
diff --git a/pkg/router/skipper.go b/pkg/router/skipper.go
index 76285dbea..50d06bf53 100644
--- a/pkg/router/skipper.go
+++ b/pkg/router/skipper.go
@@ -129,7 +129,7 @@ func (skp *SkipperRouter) Reconcile(canary *flaggerv1.Canary) error {
 	if cmp.Diff(iClone.Spec, canaryIngress.Spec) != "" {
 		ingressClone := canaryIngress.DeepCopy()
 		ingressClone.Spec = iClone.Spec
-		ingressClone.Annotations = iClone.Annotations
+		ingressClone.Annotations = makeAnnotations(iClone.Annotations)
 
 		_, err := skp.kubeClient.NetworkingV1().Ingresses(canary.Namespace).Update(context.TODO(), ingressClone, metav1.UpdateOptions{})
 		if err != nil {
diff --git a/pkg/router/traefik.go b/pkg/router/traefik.go
index b502d0a1a..ab3a79cd7 100644
--- a/pkg/router/traefik.go
+++ b/pkg/router/traefik.go
@@ -72,7 +72,7 @@ func (tr *TraefikRouter) Reconcile(canary *flaggerv1.Canary) error {
 				Name:        apexName,
 				Namespace:   canary.Namespace,
 				Labels:      tsMetadata.Labels,
-				Annotations: tsMetadata.Annotations,
+				Annotations: makeAnnotations(tsMetadata.Annotations),
 				OwnerReferences: []metav1.OwnerReference{
 					*metav1.NewControllerRef(canary, schema.GroupVersionKind{
 						Group:   flaggerv1.SchemeGroupVersion.Group,
diff --git a/pkg/router/util.go b/pkg/router/util.go
index e2bb04ee3..d6748968b 100644
--- a/pkg/router/util.go
+++ b/pkg/router/util.go
@@ -17,3 +17,15 @@ func includeLabelsByPrefix(labels map[string]string, includeLabelPrefixes []stri
 
 	return filteredLabels
 }
+
+func makeAnnotations(in map[string]string) map[string]string {
+	out := make(map[string]string)
+	for key, value := range in {
+		// skip Flux GC markers
+		if strings.Contains(key, "/checksum") {
+			continue
+		}
+		out[key] = value
+	}
+	return out
+}