diff --git a/docs/book/src/cronjob-tutorial/testdata/project/config/crd/kustomization.yaml b/docs/book/src/cronjob-tutorial/testdata/project/config/crd/kustomization.yaml
index 726852ee68b..e14663ce582 100644
--- a/docs/book/src/cronjob-tutorial/testdata/project/config/crd/kustomization.yaml
+++ b/docs/book/src/cronjob-tutorial/testdata/project/config/crd/kustomization.yaml
@@ -13,7 +13,7 @@ patches:
 
 # [CERTMANAGER] To enable cert-manager, uncomment all the sections with [CERTMANAGER] prefix.
 # patches here are for enabling the CA injection for each CRD
-- path: patches/cainjection_in_cronjobs.yaml
+#- path: patches/cainjection_in_cronjobs.yaml
 #+kubebuilder:scaffold:crdkustomizecainjectionpatch
 
 # the following config is for teaching kustomize how to do kustomization for CRDs.
diff --git a/hack/docs/internal/cronjob-tutorial/generate_cronjob.go b/hack/docs/internal/cronjob-tutorial/generate_cronjob.go
index f64a28ea3d5..08cf799b62a 100644
--- a/hack/docs/internal/cronjob-tutorial/generate_cronjob.go
+++ b/hack/docs/internal/cronjob-tutorial/generate_cronjob.go
@@ -542,22 +542,11 @@ var _ = AfterSuite(func() {
 
 func updateKustomization(sp *Sample) {
 	var err error
-	// uncomment default/kustomization
-	err = pluginutil.UncommentCode(
-		filepath.Join(sp.ctx.Dir, "config/default/kustomization.yaml"),
-		`#- ../webhook`, `#`)
-	CheckError("fixing default/kustomization", err)
-
 	err = pluginutil.UncommentCode(
 		filepath.Join(sp.ctx.Dir, "config/default/kustomization.yaml"),
 		`#- ../certmanager`, `#`)
 	CheckError("fixing default/kustomization", err)
 
-	err = pluginutil.UncommentCode(
-		filepath.Join(sp.ctx.Dir, "config/default/kustomization.yaml"),
-		`#- manager_webhook_patch.yaml`, `#`)
-	CheckError("fixing default/kustomization", err)
-
 	err = pluginutil.UncommentCode(
 		filepath.Join(sp.ctx.Dir, "config/default/kustomization.yaml"),
 		`#- webhookcainjection`, `#`)
@@ -571,18 +560,7 @@ func updateKustomization(sp *Sample) {
 	err = pluginutil.UncommentCode(
 		filepath.Join(sp.ctx.Dir, "config/default/kustomization.yaml"),
 		DefaultKustomization, `#`)
-	CheckError("fixing default/kustomization", err)
 
-	// uncomment crd/kustomization
-	err = pluginutil.UncommentCode(
-		filepath.Join(sp.ctx.Dir, "config/crd/kustomization.yaml"),
-		`#- path: patches/webhook_in_cronjobs.yaml`, `#`)
-	CheckError("fixing crd/kustomization", err)
-
-	err = pluginutil.UncommentCode(
-		filepath.Join(sp.ctx.Dir, "config/crd/kustomization.yaml"),
-		`#- path: patches/cainjection_in_cronjobs.yaml`, `#`)
-	CheckError("fixing crd/kustomization", err)
 }
 
 func updateExample(sp *Sample) {
diff --git a/pkg/plugins/common/kustomize/v2/scaffolds/webhook.go b/pkg/plugins/common/kustomize/v2/scaffolds/webhook.go
index 2dedaa52e22..6324e028c15 100644
--- a/pkg/plugins/common/kustomize/v2/scaffolds/webhook.go
+++ b/pkg/plugins/common/kustomize/v2/scaffolds/webhook.go
@@ -18,6 +18,7 @@ package scaffolds
 
 import (
 	"fmt"
+	pluginutil "sigs.k8s.io/kubebuilder/v3/pkg/plugin/util"
 
 	log "github.com/sirupsen/logrus"
 
@@ -69,6 +70,35 @@ func (s *webhookScaffolder) Scaffold() error {
 		return fmt.Errorf("error updating resource: %w", err)
 	}
 
+	kustomizeFilePath := "config/default/kustomization.yaml"
+	err := pluginutil.UncommentCode(kustomizeFilePath, "#- ../webhook", `#`)
+	if err != nil {
+		hasWebHookUncommented, err := pluginutil.HasFragment(kustomizeFilePath, "- ../webhook")
+		if !hasWebHookUncommented || err != nil {
+			log.Errorf("Unable to find the target #- ../webhook to uncomment in the file "+
+				"%s.", kustomizeFilePath)
+		}
+	}
+
+	err = pluginutil.UncommentCode(kustomizeFilePath, "#- manager_webhook_patch.yaml", `#`)
+	if err != nil {
+		hasWebHookUncommented, err := pluginutil.HasFragment(kustomizeFilePath, "- manager_webhook_patch.yaml")
+		if !hasWebHookUncommented || err != nil {
+			log.Errorf("Unable to find the target #- manager_webhook_patch.yaml to uncomment in the file "+
+				"%s.", kustomizeFilePath)
+		}
+	}
+
+	crdKustomizationsFilePath := "config/crd/kustomization.yaml"
+	err = pluginutil.UncommentCode(crdKustomizationsFilePath, "#- path: patches/webhook", `#`)
+	if err != nil {
+		hasWebHookUncommented, err := pluginutil.HasFragment(crdKustomizationsFilePath, "- path: patches/webhook")
+		if !hasWebHookUncommented || err != nil {
+			log.Errorf("Unable to find the target(s) #- path: patches/webhook/* to uncomment in the file "+
+				"%s.", crdKustomizationsFilePath)
+		}
+	}
+
 	if err := scaffold.Execute(
 		&kdefault.WebhookCAInjectionPatch{},
 		&kdefault.ManagerWebhookPatch{},
diff --git a/test/e2e/v4/generate_test.go b/test/e2e/v4/generate_test.go
index d4fc718bc25..e7056394d34 100644
--- a/test/e2e/v4/generate_test.go
+++ b/test/e2e/v4/generate_test.go
@@ -82,25 +82,12 @@ Count int `+"`"+`json:"count,omitempty"`+"`"+`
 		fmt.Sprintf("%s_webhook.go", strings.ToLower(kbc.Kind))))
 	ExpectWithOffset(1, err).NotTo(HaveOccurred())
 
-	By("uncomment kustomization.yaml to enable webhook and ca injection")
-	ExpectWithOffset(1, pluginutil.UncommentCode(
-		filepath.Join(kbc.Dir, "config", "crd", "kustomization.yaml"),
-		fmt.Sprintf("#- path: patches/webhook_in_%s.yaml", kbc.Resources), "#")).To(Succeed())
-	ExpectWithOffset(1, pluginutil.UncommentCode(
-		filepath.Join(kbc.Dir, "config", "crd", "kustomization.yaml"),
-		fmt.Sprintf("#- path: patches/cainjection_in_%s.yaml", kbc.Resources), "#")).To(Succeed())
-	ExpectWithOffset(1, pluginutil.UncommentCode(
-		filepath.Join(kbc.Dir, "config", "default", "kustomization.yaml"),
-		"#- ../webhook", "#")).To(Succeed())
 	ExpectWithOffset(1, pluginutil.UncommentCode(
 		filepath.Join(kbc.Dir, "config", "default", "kustomization.yaml"),
 		"#- ../certmanager", "#")).To(Succeed())
 	ExpectWithOffset(1, pluginutil.UncommentCode(
 		filepath.Join(kbc.Dir, "config", "default", "kustomization.yaml"),
 		"#- ../prometheus", "#")).To(Succeed())
-	ExpectWithOffset(1, pluginutil.UncommentCode(
-		filepath.Join(kbc.Dir, "config", "default", "kustomization.yaml"),
-		"#- manager_webhook_patch.yaml", "#")).To(Succeed())
 	ExpectWithOffset(1, pluginutil.UncommentCode(
 		filepath.Join(kbc.Dir, "config", "default", "kustomization.yaml"),
 		"#- webhookcainjection_patch.yaml", "#")).To(Succeed())
diff --git a/testdata/project-v4-multigroup/config/crd/kustomization.yaml b/testdata/project-v4-multigroup/config/crd/kustomization.yaml
index e3729c3f731..edb4eaf7c9b 100644
--- a/testdata/project-v4-multigroup/config/crd/kustomization.yaml
+++ b/testdata/project-v4-multigroup/config/crd/kustomization.yaml
@@ -19,12 +19,12 @@ resources:
 patches:
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix.
 # patches here are for enabling the conversion webhook for each CRD
-#- path: patches/webhook_in_crew_captains.yaml
-#- path: patches/webhook_in_ship_frigates.yaml
-#- path: patches/webhook_in_ship_destroyers.yaml
-#- path: patches/webhook_in_ship_cruisers.yaml
-#- path: patches/webhook_in_sea-creatures_krakens.yaml
-#- path: patches/webhook_in_sea-creatures_leviathans.yaml
+- path: patches/webhook_in_crew_captains.yaml
+- path: patches/webhook_in_ship_frigates.yaml
+- path: patches/webhook_in_ship_destroyers.yaml
+- path: patches/webhook_in_ship_cruisers.yaml
+- path: patches/webhook_in_sea-creatures_krakens.yaml
+- path: patches/webhook_in_sea-creatures_leviathans.yaml
 #- path: patches/webhook_in_foo.policy_healthcheckpolicies.yaml
 #- path: patches/webhook_in_foo_bars.yaml
 #- path: patches/webhook_in_fiz_bars.yaml
diff --git a/testdata/project-v4-multigroup/config/default/kustomization.yaml b/testdata/project-v4-multigroup/config/default/kustomization.yaml
index baea92fc167..ce2920a1301 100644
--- a/testdata/project-v4-multigroup/config/default/kustomization.yaml
+++ b/testdata/project-v4-multigroup/config/default/kustomization.yaml
@@ -20,7 +20,7 @@ resources:
 - ../manager
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
-#- ../webhook
+- ../webhook
 # [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER'. 'WEBHOOK' components are required.
 #- ../certmanager
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
@@ -36,7 +36,7 @@ patchesStrategicMerge:
 
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
-#- manager_webhook_patch.yaml
+- manager_webhook_patch.yaml
 
 # [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER'.
 # Uncomment 'CERTMANAGER' sections in crd/kustomization.yaml to enable the CA injection in the admission webhooks.
diff --git a/testdata/project-v4-with-deploy-image/config/crd/kustomization.yaml b/testdata/project-v4-with-deploy-image/config/crd/kustomization.yaml
index 1385006e680..c4fb2e1b99b 100644
--- a/testdata/project-v4-with-deploy-image/config/crd/kustomization.yaml
+++ b/testdata/project-v4-with-deploy-image/config/crd/kustomization.yaml
@@ -9,7 +9,7 @@ resources:
 patches:
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix.
 # patches here are for enabling the conversion webhook for each CRD
-#- path: patches/webhook_in_memcacheds.yaml
+- path: patches/webhook_in_memcacheds.yaml
 #- path: patches/webhook_in_busyboxes.yaml
 #+kubebuilder:scaffold:crdkustomizewebhookpatch
 
diff --git a/testdata/project-v4-with-deploy-image/config/default/kustomization.yaml b/testdata/project-v4-with-deploy-image/config/default/kustomization.yaml
index faf2235f91f..9a8d7b34515 100644
--- a/testdata/project-v4-with-deploy-image/config/default/kustomization.yaml
+++ b/testdata/project-v4-with-deploy-image/config/default/kustomization.yaml
@@ -20,7 +20,7 @@ resources:
 - ../manager
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
-#- ../webhook
+- ../webhook
 # [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER'. 'WEBHOOK' components are required.
 #- ../certmanager
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
@@ -36,7 +36,7 @@ patchesStrategicMerge:
 
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
-#- manager_webhook_patch.yaml
+- manager_webhook_patch.yaml
 
 # [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER'.
 # Uncomment 'CERTMANAGER' sections in crd/kustomization.yaml to enable the CA injection in the admission webhooks.
diff --git a/testdata/project-v4/config/crd/kustomization.yaml b/testdata/project-v4/config/crd/kustomization.yaml
index a67f99e5ea3..55a06bf09c9 100644
--- a/testdata/project-v4/config/crd/kustomization.yaml
+++ b/testdata/project-v4/config/crd/kustomization.yaml
@@ -10,9 +10,9 @@ resources:
 patches:
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix.
 # patches here are for enabling the conversion webhook for each CRD
-#- path: patches/webhook_in_captains.yaml
-#- path: patches/webhook_in_firstmates.yaml
-#- path: patches/webhook_in_admirales.yaml
+- path: patches/webhook_in_captains.yaml
+- path: patches/webhook_in_firstmates.yaml
+- path: patches/webhook_in_admirales.yaml
 #+kubebuilder:scaffold:crdkustomizewebhookpatch
 
 # [CERTMANAGER] To enable cert-manager, uncomment all the sections with [CERTMANAGER] prefix.
diff --git a/testdata/project-v4/config/default/kustomization.yaml b/testdata/project-v4/config/default/kustomization.yaml
index 1516d32747f..c96e5df1142 100644
--- a/testdata/project-v4/config/default/kustomization.yaml
+++ b/testdata/project-v4/config/default/kustomization.yaml
@@ -20,7 +20,7 @@ resources:
 - ../manager
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
-#- ../webhook
+- ../webhook
 # [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER'. 'WEBHOOK' components are required.
 #- ../certmanager
 # [PROMETHEUS] To enable prometheus monitor, uncomment all sections with 'PROMETHEUS'.
@@ -36,7 +36,7 @@ patchesStrategicMerge:
 
 # [WEBHOOK] To enable webhook, uncomment all the sections with [WEBHOOK] prefix including the one in
 # crd/kustomization.yaml
-#- manager_webhook_patch.yaml
+- manager_webhook_patch.yaml
 
 # [CERTMANAGER] To enable cert-manager, uncomment all sections with 'CERTMANAGER'.
 # Uncomment 'CERTMANAGER' sections in crd/kustomization.yaml to enable the CA injection in the admission webhooks.