diff --git a/pkg/deploy/deploy.go b/pkg/deploy/deploy.go
index 44a63511fbe..672adb50c8a 100644
--- a/pkg/deploy/deploy.go
+++ b/pkg/deploy/deploy.go
@@ -257,8 +257,11 @@ func manageResource(ctx context.Context, cli client.Client, obj *unstructured.Un
 	// Create the resource if it doesn't exist and component is enabled
 	if apierrs.IsNotFound(err) {
 		// Set the owner reference for garbage collection
-		if err = ctrl.SetControllerReference(owner, metav1.Object(obj), cli.Scheme()); err != nil {
-			return err
+		// Skip set on CRD, e.g we should not delete notebook CRD if we delete DSC instance
+		if found.GetKind() != "CustomResourceDefinition" {
+			if err = ctrl.SetControllerReference(owner, metav1.Object(obj), cli.Scheme()); err != nil {
+				return err
+			}
 		}
 
 		return cli.Create(ctx, obj)