diff --git a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/kustomization.go b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/kustomization.go
index b77d2137b97..2da3a06a8cb 100644
--- a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/kustomization.go
+++ b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/crd/kustomization.go
@@ -91,7 +91,11 @@ func (f *Kustomization) GetCodeFragments() machinery.CodeFragmentsMap {
 
 	if !f.Resource.Webhooks.IsEmpty() {
 		webhookPatch := fmt.Sprintf(webhookPatchCodeFragment, suffix)
-		fragments[machinery.NewMarkerFor(f.Path, webhookPatchMarker)] = []string{webhookPatch}
+
+		marker := machinery.NewMarkerFor(f.Path, webhookPatchMarker)
+		if _, exists := fragments[marker]; !exists {
+			fragments[marker] = []string{webhookPatch}
+		}
 	}
 
 	// Generate resource code fragments