diff --git a/.github/workflows/test-e2e-samples.yml b/.github/workflows/test-e2e-samples.yml
index 97be2426b9f..24926378ee9 100644
--- a/.github/workflows/test-e2e-samples.yml
+++ b/.github/workflows/test-e2e-samples.yml
@@ -39,12 +39,6 @@ jobs:
 
       - name: Prepare project-v4
         run: |
-          KUSTOMIZATION_FILE_PATH="testdata/project-v4/config/default/kustomization.yaml"
-          sed -i '25s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '47,49s/^#//' $KUSTOMIZATION_FILE_PATH
-          # Uncomment all cert-manager injections
-          sed -i '59,234s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '236,251s/^#//' $KUSTOMIZATION_FILE_PATH
           cd testdata/project-v4/
           go mod tidy
 
@@ -81,17 +75,6 @@ jobs:
 
       - name: Prepare project-v4-with-plugins
         run: |
-          KUSTOMIZATION_FILE_PATH="testdata/project-v4-with-plugins/config/default/kustomization.yaml"
-          sed -i '25s/^#//' $KUSTOMIZATION_FILE_PATH
-          # Uncomment only ValidatingWebhookConfiguration
-          # from cert-manager replaces; we are leaving defaulting uncommented
-          # since this sample has no defaulting webhooks
-          sed -i '59,77s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '90,107s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '120,186s/^#//' $KUSTOMIZATION_FILE_PATH
-          # Uncomment only --conversion webhooks CA injection
-          sed -i '219,234s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '236,251s/^#//' $KUSTOMIZATION_FILE_PATH
           cd testdata/project-v4-with-plugins/
           go mod tidy
 
@@ -128,13 +111,6 @@ jobs:
 
       - name: Prepare project-v4-multigroup
         run: |
-          KUSTOMIZATION_FILE_PATH="testdata/project-v4-multigroup/config/default/kustomization.yaml"
-          sed -i '25s/^#//' $KUSTOMIZATION_FILE_PATH
-          # Uncomment all cert-manager injections for webhooks only
-          sed -i '59,77s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '90,107s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '120,234s/^#//' $KUSTOMIZATION_FILE_PATH
-          sed -i '236,251s/^#//' $KUSTOMIZATION_FILE_PATH
           cd testdata/project-v4-multigroup
           go mod tidy
 
diff --git a/pkg/plugins/golang/v4/scaffolds/webhook.go b/pkg/plugins/golang/v4/scaffolds/webhook.go
index d4588921c81..2485c00794c 100644
--- a/pkg/plugins/golang/v4/scaffolds/webhook.go
+++ b/pkg/plugins/golang/v4/scaffolds/webhook.go
@@ -173,5 +173,243 @@ You need to implement the conversion.Hub and conversion.Convertible interfaces f
 			}
 		}
 	}
+
+	kustomizeFilePath := "config/default/kustomization.yaml"
+	webhookConfig := []string{
+		"#- ../webhook",
+		"#- ../certmanager",
+		webhookTarget,
+	}
+	for _, config := range webhookConfig {
+		if err := pluginutil.UncommentCode(kustomizeFilePath, config, "#"); err != nil {
+			log.Errorf("Unable to uncomment %s in the file %s.", config, kustomizeFilePath)
+		}
+	}
+
+	prometheusKustomizeFilePath := "config/prometheus/kustomization.yaml"
+	if err := pluginutil.UncommentCode(prometheusKustomizeFilePath, prometheusTarget, "#"); err != nil {
+		log.Errorf("Unable to uncomment resources: in the file %s.", prometheusKustomizeFilePath)
+	}
+
+	if doDefaulting {
+		if err := pluginutil.UncommentCode(kustomizeFilePath, defaultingWebhookTarget, "#"); err != nil {
+			if err := pluginutil.UncommentCode(kustomizeFilePath, defaultingWebhookTarget, "#"); err != nil {
+				log.Errorf("Unable to uncomment %s in the file %s.", defaultingWebhookTarget, kustomizeFilePath)
+			}
+
+		}
+	}
+	if doConversion {
+		if err := pluginutil.UncommentCode(kustomizeFilePath, conversionWebhookTarget, "#"); err != nil {
+			log.Errorf("Unable to uncomment %s in the file %s.", conversionWebhookTarget, kustomizeFilePath)
+		}
+	}
+
+	if doValidation {
+		if err := pluginutil.UncommentCode(kustomizeFilePath, validationWebhookTarget, "#"); err != nil {
+			log.Errorf("Unable to uncomment %s in the file %s.", validationWebhookTarget, kustomizeFilePath)
+		}
+	}
 	return nil
+
 }
+
+const webhookTarget = `#replacements:
+# - source: # Uncomment the following block to enable certificates for metrics
+#     kind: Service
+#     version: v1
+#     name: controller-manager-metrics-service
+#     fieldPath: metadata.name
+#   targets:
+#     - select:
+#         kind: Certificate
+#         group: cert-manager.io
+#         version: v1
+#         name: metrics-certs
+#       fieldPaths:
+#         - spec.dnsNames.0
+#         - spec.dnsNames.1
+#       options:
+#         delimiter: '.'
+#         index: 0
+#         create: true
+#     - select:
+#         kind: ServiceMonitor
+#         group: monitoring.coreos.com
+#         version: v1
+#         name: controller-manager-metrics-monitor
+#       fieldPaths:
+#         - spec.endpoints.0.tlsConfig.serverName
+#       options:
+#         delimiter: '.'
+#         index: 0
+#         create: true
+#
+# - source:
+#     kind: Service
+#     version: v1
+#     name: controller-manager-metrics-service
+#     fieldPath: metadata.namespace
+#   targets:
+#     - select:
+#         kind: Certificate
+#         group: cert-manager.io
+#         version: v1
+#         name: metrics-certs
+#       fieldPaths:
+#         - spec.dnsNames.0
+#         - spec.dnsNames.1
+#       options:
+#         delimiter: '.'
+#         index: 1
+#         create: true
+#     - select:
+#         kind: ServiceMonitor
+#         group: monitoring.coreos.com
+#         version: v1
+#         name: controller-manager-metrics-monitor
+#       fieldPaths:
+#         - spec.endpoints.0.tlsConfig.serverName
+#       options:
+#         delimiter: '.'
+#         index: 1
+#         create: true
+#
+# - source: # Uncomment the following block if you have any webhook
+#     kind: Service
+#     version: v1
+#     name: webhook-service
+#     fieldPath: .metadata.name # Name of the service
+#   targets:
+#     - select:
+#         kind: Certificate
+#         group: cert-manager.io
+#         version: v1
+#         name: serving-cert
+#       fieldPaths:
+#         - .spec.dnsNames.0
+#         - .spec.dnsNames.1
+#       options:
+#         delimiter: '.'
+#         index: 0
+#         create: true
+# - source:
+#     kind: Service
+#     version: v1
+#     name: webhook-service
+#     fieldPath: .metadata.namespace # Namespace of the service
+#   targets:
+#     - select:
+#         kind: Certificate
+#         group: cert-manager.io
+#         version: v1
+#         name: serving-cert
+#       fieldPaths:
+#         - .spec.dnsNames.0
+#         - .spec.dnsNames.1
+#       options:
+#         delimiter: '.'
+#         index: 1
+#         create: true`
+
+const prometheusTarget = `#patches:
+#  - path: monitor_tls_patch.yaml
+#    target:
+#      kind: ServiceMonitor
+`
+
+const defaultingWebhookTarget = `# - source: # Uncomment the following block if you have a DefaultingWebhook (--defaulting )
+#     kind: Certificate
+#     group: cert-manager.io
+#     version: v1
+#     name: serving-cert
+#     fieldPath: .metadata.namespace # Namespace of the certificate CR
+#   targets:
+#     - select:
+#         kind: MutatingWebhookConfiguration
+#       fieldPaths:
+#         - .metadata.annotations.[cert-manager.io/inject-ca-from]
+#       options:
+#         delimiter: '/'
+#         index: 0
+#         create: true
+# - source:
+#     kind: Certificate
+#     group: cert-manager.io
+#     version: v1
+#     name: serving-cert
+#     fieldPath: .metadata.name
+#   targets:
+#     - select:
+#         kind: MutatingWebhookConfiguration
+#       fieldPaths:
+#         - .metadata.annotations.[cert-manager.io/inject-ca-from]
+#       options:
+#         delimiter: '/'
+#         index: 1
+#         create: true`
+
+const conversionWebhookTarget = `# - source: # Uncomment the following block if you have a ConversionWebhook (--conversion)
+#     kind: Certificate
+#     group: cert-manager.io
+#     version: v1
+#     name: serving-cert
+#     fieldPath: .metadata.namespace # Namespace of the certificate CR
+#   targets: # Do not remove or uncomment the following scaffold marker; required to generate code for target CRD.
+#     - select:
+#         kind: CustomResourceDefinition
+#         name: guestbooks.webapp.my.domain
+#       fieldPaths:
+#         - .metadata.annotations.[cert-manager.io/inject-ca-from]
+#       options:
+#         delimiter: '/'
+#         index: 0
+#         create: true
+# +kubebuilder:scaffold:crdkustomizecainjectionns
+# - source:
+#     kind: Certificate
+#     group: cert-manager.io
+#     version: v1
+#     name: serving-cert
+#     fieldPath: .metadata.name
+#   targets: # Do not remove or uncomment the following scaffold marker; required to generate code for target CRD.
+#     - select:
+#         kind: CustomResourceDefinition
+#         name: guestbooks.webapp.my.domain
+#       fieldPaths:
+#         - .metadata.annotations.[cert-manager.io/inject-ca-from]
+#       options:
+#         delimiter: '/'
+#         index: 1
+#         create: true`
+
+const validationWebhookTarget = `# - source: # Uncomment the following block if you have a ValidatingWebhook (--programmatic-validation)
+#     kind: Certificate
+#     group: cert-manager.io
+#     version: v1
+#     name: serving-cert # This name should match the one in certificate.yaml
+#     fieldPath: .metadata.namespace # Namespace of the certificate CR
+#   targets:
+#     - select:
+#         kind: ValidatingWebhookConfiguration
+#       fieldPaths:
+#         - .metadata.annotations.[cert-manager.io/inject-ca-from]
+#       options:
+#         delimiter: '/'
+#         index: 0
+#         create: true
+# - source:
+#     kind: Certificate
+#     group: cert-manager.io
+#     version: v1
+#     name: serving-cert
+#     fieldPath: .metadata.name
+#   targets:
+#     - select:
+#         kind: ValidatingWebhookConfiguration
+#       fieldPaths:
+#         - .metadata.annotations.[cert-manager.io/inject-ca-from]
+#       options:
+#         delimiter: '/'
+#         index: 1
+#         create: true`