diff --git a/config/crd/kustomization.yaml b/config/crd/kustomization.yaml
index dd31bed4..786b767d 100644
--- a/config/crd/kustomization.yaml
+++ b/config/crd/kustomization.yaml
@@ -1,3 +1,6 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
 # This kustomization.yaml is not intended to be run by itself,
 # since it depends on service name and namespace that are out of this kustomize package.
 # It should be run by config/default
@@ -5,7 +8,7 @@ resources:
 - bases/confidentialcontainers.org_ccruntimes.yaml
 #+kubebuilder:scaffold:crdkustomizeresource
 
-patchesStrategicMerge:
+patches:
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix.
 # patches here are for enabling the conversion webhook for each CRD
 #- patches/webhook_in_ccruntimes.yaml
diff --git a/config/default/kustomization.yaml b/config/default/kustomization.yaml
index 88dc7a9d..2d01b904 100644
--- a/config/default/kustomization.yaml
+++ b/config/default/kustomization.yaml
@@ -1,3 +1,5 @@
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
 # Adds namespace to all resources.
 namespace: confidential-containers-system
 
@@ -12,7 +14,7 @@ namePrefix: cc-operator-
 #commonLabels:
 #  someName: someValue
 
-bases:
+resources:
 - ../crd
 - ../rbac
 - ../manager
@@ -24,11 +26,11 @@ bases:
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
 #- ../prometheus
 
-patchesStrategicMerge:
+patches:
 # Protect the /metrics endpoint by putting it behind auth.
 # If you want your controller-manager to expose the /metrics
 # endpoint w/o any authn/z, please comment the following line.
-- manager_auth_proxy_patch.yaml
+- path: manager_auth_proxy_patch.yaml
 
 # Mount the controller config file for loading manager configurations
 # through a ComponentConfig type
diff --git a/config/samples/enclave-cc/hw/kustomization.yaml b/config/samples/enclave-cc/hw/kustomization.yaml
index 9d80e03e..ea280be8 100644
--- a/config/samples/enclave-cc/hw/kustomization.yaml
+++ b/config/samples/enclave-cc/hw/kustomization.yaml
@@ -1,4 +1,7 @@
-bases:
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+
+resources:
 - ../base
 
 nameSuffix: -sgx-mode-hw