diff --git a/pkg/plugins/golang/v3/scaffolds/init.go b/pkg/plugins/golang/v3/scaffolds/init.go
index 1b7b6ece584..76dca0426f6 100644
--- a/pkg/plugins/golang/v3/scaffolds/init.go
+++ b/pkg/plugins/golang/v3/scaffolds/init.go
@@ -25,7 +25,6 @@ import (
 	"sigs.k8s.io/kubebuilder/v3/pkg/machinery"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates"
-	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/config/kdefault"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/config/manager"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/config/prometheus"
@@ -132,8 +131,5 @@ func (s *initScaffolder) Scaffold() error {
 		&kdefault.ManagerConfigPatch{},
 		&prometheus.Kustomization{},
 		&prometheus.Monitor{},
-		&certmanager.Certificate{},
-		&certmanager.Kustomization{},
-		&certmanager.KustomizeConfig{},
 	)
 }
diff --git a/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/certificate.go b/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/certificate.go
index 76c2b186f65..fc449472db2 100644
--- a/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/certificate.go
+++ b/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/certificate.go
@@ -37,6 +37,9 @@ func (f *Certificate) SetTemplateDefaults() error {
 
 	f.TemplateBody = certManagerTemplate
 
+	// If file exists (ex. because a webhook was already created), skip creation.
+	f.IfExistsAction = machinery.SkipFile
+
 	return nil
 }
 
diff --git a/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomization.go b/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomization.go
index 522bdd9b67f..2e31a62d4ae 100644
--- a/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomization.go
+++ b/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomization.go
@@ -37,6 +37,9 @@ func (f *Kustomization) SetTemplateDefaults() error {
 
 	f.TemplateBody = kustomizationTemplate
 
+	// If file exists (ex. because a webhook was already created), skip creation.
+	f.IfExistsAction = machinery.SkipFile
+
 	return nil
 }
 
diff --git a/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomizeconfig.go b/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomizeconfig.go
index 573a7e8f602..02bda5e7341 100644
--- a/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomizeconfig.go
+++ b/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager/kustomizeconfig.go
@@ -37,6 +37,9 @@ func (f *KustomizeConfig) SetTemplateDefaults() error {
 
 	f.TemplateBody = kustomizeConfigTemplate
 
+	// If file exists (ex. because a webhook was already created), skip creation.
+	f.IfExistsAction = machinery.SkipFile
+
 	return nil
 }
 
diff --git a/pkg/plugins/golang/v3/scaffolds/webhook.go b/pkg/plugins/golang/v3/scaffolds/webhook.go
index 51a020e1495..7035f50029c 100644
--- a/pkg/plugins/golang/v3/scaffolds/webhook.go
+++ b/pkg/plugins/golang/v3/scaffolds/webhook.go
@@ -27,6 +27,7 @@ import (
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/api"
+	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/config/certmanager"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/config/kdefault"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/config/webhook"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v3/scaffolds/internal/templates/hack"
@@ -93,6 +94,9 @@ func (s *webhookScaffolder) Scaffold() error {
 		&webhook.Kustomization{Force: s.force},
 		&webhook.KustomizeConfig{},
 		&webhook.Service{},
+		&certmanager.Certificate{},
+		&certmanager.Kustomization{},
+		&certmanager.KustomizeConfig{},
 	); err != nil {
 		return err
 	}
diff --git a/testdata/project-v3-addon/config/certmanager/certificate.yaml b/testdata/project-v3-addon/config/certmanager/certificate.yaml
deleted file mode 100644
index 52d866183c7..00000000000
--- a/testdata/project-v3-addon/config/certmanager/certificate.yaml
+++ /dev/null
@@ -1,25 +0,0 @@
-# The following manifests contain a self-signed issuer CR and a certificate CR.
-# More document can be found at https://docs.cert-manager.io
-# WARNING: Targets CertManager v1.0. Check https://cert-manager.io/docs/installation/upgrading/ for breaking changes.
-apiVersion: cert-manager.io/v1
-kind: Issuer
-metadata:
-  name: selfsigned-issuer
-  namespace: system
-spec:
-  selfSigned: {}
----
-apiVersion: cert-manager.io/v1
-kind: Certificate
-metadata:
-  name: serving-cert  # this name should match the one appeared in kustomizeconfig.yaml
-  namespace: system
-spec:
-  # $(SERVICE_NAME) and $(SERVICE_NAMESPACE) will be substituted by kustomize
-  dnsNames:
-  - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc
-  - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc.cluster.local
-  issuerRef:
-    kind: Issuer
-    name: selfsigned-issuer
-  secretName: webhook-server-cert # this secret will not be prefixed, since it's not managed by kustomize
diff --git a/testdata/project-v3-addon/config/certmanager/kustomization.yaml b/testdata/project-v3-addon/config/certmanager/kustomization.yaml
deleted file mode 100644
index bebea5a595e..00000000000
--- a/testdata/project-v3-addon/config/certmanager/kustomization.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-resources:
-- certificate.yaml
-
-configurations:
-- kustomizeconfig.yaml
diff --git a/testdata/project-v3-addon/config/certmanager/kustomizeconfig.yaml b/testdata/project-v3-addon/config/certmanager/kustomizeconfig.yaml
deleted file mode 100644
index 90d7c313ca1..00000000000
--- a/testdata/project-v3-addon/config/certmanager/kustomizeconfig.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-# This configuration is for teaching kustomize how to update name ref and var substitution 
-nameReference:
-- kind: Issuer
-  group: cert-manager.io
-  fieldSpecs:
-  - kind: Certificate
-    group: cert-manager.io
-    path: spec/issuerRef/name
-
-varReference:
-- kind: Certificate
-  group: cert-manager.io
-  path: spec/commonName
-- kind: Certificate
-  group: cert-manager.io
-  path: spec/dnsNames