diff --git a/docs/book/src/cronjob-tutorial/testdata/project/config/default/manager_metrics_patch.yaml b/docs/book/src/cronjob-tutorial/testdata/project/config/default/manager_metrics_patch.yaml
index ee197d3f718..4cc88a79951 100644
--- a/docs/book/src/cronjob-tutorial/testdata/project/config/default/manager_metrics_patch.yaml
+++ b/docs/book/src/cronjob-tutorial/testdata/project/config/default/manager_metrics_patch.yaml
@@ -10,4 +10,9 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"
diff --git a/docs/book/src/getting-started/testdata/project/config/default/manager_metrics_patch.yaml b/docs/book/src/getting-started/testdata/project/config/default/manager_metrics_patch.yaml
index ee197d3f718..4cc88a79951 100644
--- a/docs/book/src/getting-started/testdata/project/config/default/manager_metrics_patch.yaml
+++ b/docs/book/src/getting-started/testdata/project/config/default/manager_metrics_patch.yaml
@@ -10,4 +10,9 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"
diff --git a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enable_matrics_patch.go b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enable_matrics_patch.go
index 768950bbf04..a7cb55ef602 100644
--- a/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enable_matrics_patch.go
+++ b/pkg/plugins/common/kustomize/v2/scaffolds/internal/templates/config/kdefault/enable_matrics_patch.go
@@ -54,5 +54,10 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"
 `
diff --git a/test/e2e/v4/plugin_cluster_test.go b/test/e2e/v4/plugin_cluster_test.go
index 6c3fcddda18..cd2520eb671 100644
--- a/test/e2e/v4/plugin_cluster_test.go
+++ b/test/e2e/v4/plugin_cluster_test.go
@@ -163,6 +163,20 @@ func Run(kbc *utils.TestContext, hasWebhook, isToUseInstaller, hasMetrics bool)
 	}()
 	EventuallyWithOffset(1, verifyControllerUp, time.Minute, time.Second).Should(Succeed())
 
+	By("Checking if all flags are applied to the manager pod")
+
+	// Get the manager pod details
+	podOutput, err := kbc.Kubectl.Get(
+		true,
+		"pod", controllerPodName,
+		"-o", "jsonpath={.spec.containers[0].args}",
+	)
+	ExpectWithOffset(1, err).NotTo(HaveOccurred())
+	ExpectWithOffset(1, podOutput).To(ContainSubstring("--leader-elect"),
+		"Expected manager pod to have --leader-elect flag")
+	ExpectWithOffset(1, podOutput).To(ContainSubstring("--health-probe-bind-address=:8081"),
+		"Expected manager pod to have --health-probe-bind-address flag")
+
 	By("validating the metrics endpoint")
 	_ = curlMetrics(kbc, hasMetrics)
 
diff --git a/testdata/project-v4-multigroup-with-deploy-image/config/default/manager_metrics_patch.yaml b/testdata/project-v4-multigroup-with-deploy-image/config/default/manager_metrics_patch.yaml
index ee197d3f718..4cc88a79951 100644
--- a/testdata/project-v4-multigroup-with-deploy-image/config/default/manager_metrics_patch.yaml
+++ b/testdata/project-v4-multigroup-with-deploy-image/config/default/manager_metrics_patch.yaml
@@ -10,4 +10,9 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"
diff --git a/testdata/project-v4-multigroup/config/default/manager_metrics_patch.yaml b/testdata/project-v4-multigroup/config/default/manager_metrics_patch.yaml
index ee197d3f718..4cc88a79951 100644
--- a/testdata/project-v4-multigroup/config/default/manager_metrics_patch.yaml
+++ b/testdata/project-v4-multigroup/config/default/manager_metrics_patch.yaml
@@ -10,4 +10,9 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"
diff --git a/testdata/project-v4-with-deploy-image/config/default/manager_metrics_patch.yaml b/testdata/project-v4-with-deploy-image/config/default/manager_metrics_patch.yaml
index ee197d3f718..4cc88a79951 100644
--- a/testdata/project-v4-with-deploy-image/config/default/manager_metrics_patch.yaml
+++ b/testdata/project-v4-with-deploy-image/config/default/manager_metrics_patch.yaml
@@ -10,4 +10,9 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"
diff --git a/testdata/project-v4-with-grafana/config/default/manager_metrics_patch.yaml b/testdata/project-v4-with-grafana/config/default/manager_metrics_patch.yaml
index ee197d3f718..4cc88a79951 100644
--- a/testdata/project-v4-with-grafana/config/default/manager_metrics_patch.yaml
+++ b/testdata/project-v4-with-grafana/config/default/manager_metrics_patch.yaml
@@ -10,4 +10,9 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"
diff --git a/testdata/project-v4/config/default/manager_metrics_patch.yaml b/testdata/project-v4/config/default/manager_metrics_patch.yaml
index ee197d3f718..4cc88a79951 100644
--- a/testdata/project-v4/config/default/manager_metrics_patch.yaml
+++ b/testdata/project-v4/config/default/manager_metrics_patch.yaml
@@ -10,4 +10,9 @@ spec:
       containers:
       - name: manager
         args:
-        - "--metrics-bind-address=0.0.0.0:8080"
+          - --metrics-bind-address=0.0.0.0:8080
+          # We need to keep the same args
+          # provided in the manager.
+          # More info: https://github.com/kubernetes-sigs/kubebuilder/issues/3934
+          - --leader-elect
+          - --health-probe-bind-address=:8081"