diff --git a/config/crd/kustomization.yaml b/config/crd/kustomization.yaml
index 72215087..d1f8657d 100644
--- a/config/crd/kustomization.yaml
+++ b/config/crd/kustomization.yaml
@@ -6,7 +6,6 @@ resources:
 - bases/fence-agents-remediation.medik8s.io_fenceagentsremediationtemplates.yaml
 #+kubebuilder:scaffold:crdkustomizeresource
 
-patchesStrategicMerge:
 # [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_fenceagentsremediations.yaml
@@ -22,3 +21,5 @@ patchesStrategicMerge:
 # the following config is for teaching kustomize how to do kustomization for CRDs.
 configurations:
 - kustomizeconfig.yaml
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
diff --git a/config/default/kustomization.yaml b/config/default/kustomization.yaml
index de2fb287..036119cb 100644
--- a/config/default/kustomization.yaml
+++ b/config/default/kustomization.yaml
@@ -10,13 +10,7 @@ namePrefix: fence-agents-remediation-
 
 # Labels to add to all resources and selectors.
 #commonLabels:
-commonLabels:
-  app: "fence-agents-remediation-operator"
 
-bases:
-- ../crd
-- ../rbac
-- ../manager
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
 #- ../webhook
@@ -25,11 +19,9 @@ bases:
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
 #- ../prometheus
 
-patchesStrategicMerge:
 # 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
 
 # Mount the controller config file for loading manager configurations
 # through a ComponentConfig type
@@ -45,31 +37,15 @@ patchesStrategicMerge:
 #- webhookcainjection_patch.yaml
 
 # the following config is for teaching kustomize how to do var substitution
-vars:
-# [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER' prefix.
-#- name: CERTIFICATE_NAMESPACE # namespace of the certificate CR
-#  objref:
-#    kind: Certificate
-#    group: cert-manager.io
-#    version: v1
-#    name: serving-cert # this name should match the one in certificate.yaml
-#  fieldref:
-#    fieldpath: metadata.namespace
-#- name: CERTIFICATE_NAME
-#  objref:
-#    kind: Certificate
-#    group: cert-manager.io
-#    version: v1
-#    name: serving-cert # this name should match the one in certificate.yaml
-#- name: SERVICE_NAMESPACE # namespace of the service
-#  objref:
-#    kind: Service
-#    version: v1
-#    name: webhook-service
-#  fieldref:
-#    fieldpath: metadata.namespace
-#- name: SERVICE_NAME
-#  objref:
-#    kind: Service
-#    version: v1
-#    name: webhook-service
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+resources:
+- ../crd
+- ../rbac
+- ../manager
+labels:
+- includeSelectors: true
+  pairs:
+    app: fence-agents-remediation-operator
+patches:
+- path: manager_auth_proxy_patch.yaml
diff --git a/config/manifests/kustomization.yaml b/config/manifests/kustomization.yaml
index ecbb499f..234c6265 100644
--- a/config/manifests/kustomization.yaml
+++ b/config/manifests/kustomization.yaml
@@ -5,23 +5,5 @@ resources:
 - ../default
 - ../samples
 - ../scorecard
-
-# [WEBHOOK] To enable webhooks, uncomment all the sections with [WEBHOOK] prefix.
-# Do NOT uncomment sections with prefix [CERTMANAGER], as OLM does not support cert-manager.
-# These patches remove the unnecessary "cert" volume and its manager container volumeMount.
-#patchesJson6902:
-#- target:
-#    group: apps
-#    version: v1
-#    kind: Deployment
-#    name: controller-manager
-#    namespace: system
-#  patch: |-
-#    # Remove the manager container's "cert" volumeMount, since OLM will create and mount a set of certs.
-#    # Update the indices in this path if adding or removing containers/volumeMounts in the manager's Deployment.
-#    - op: remove
-#      path: /spec/template/spec/containers/1/volumeMounts/0
-#    # Remove the "cert" volume, since OLM will create and mount a set of certs.
-#    # Update the indices in this path if adding or removing volumes in the manager's Deployment.
-#    - op: remove
-#      path: /spec/template/spec/volumes/0
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
diff --git a/config/scorecard/kustomization.yaml b/config/scorecard/kustomization.yaml
index 50cd2d08..61ceb4d7 100644
--- a/config/scorecard/kustomization.yaml
+++ b/config/scorecard/kustomization.yaml
@@ -1,16 +1,17 @@
 resources:
 - bases/config.yaml
-patchesJson6902:
+apiVersion: kustomize.config.k8s.io/v1beta1
+kind: Kustomization
+patches:
 - path: patches/basic.config.yaml
   target:
     group: scorecard.operatorframework.io
-    version: v1alpha3
     kind: Configuration
     name: config
+    version: v1alpha3
 - path: patches/olm.config.yaml
   target:
     group: scorecard.operatorframework.io
-    version: v1alpha3
     kind: Configuration
     name: config
-#+kubebuilder:scaffold:patchesJson6902
+    version: v1alpha3