diff --git a/cmd/clusterctl/client/repository/components.go b/cmd/clusterctl/client/repository/components.go
index 92efe7a9a1de..807a17e1c720 100644
--- a/cmd/clusterctl/client/repository/components.go
+++ b/cmd/clusterctl/client/repository/components.go
@@ -42,16 +42,12 @@ const (
 	clusterRoleKind                    = "ClusterRole"
 	clusterRoleBindingKind             = "ClusterRoleBinding"
 	roleBindingKind                    = "RoleBinding"
+	certificateKind                    = "Certificate"
 	mutatingWebhookConfigurationKind   = "MutatingWebhookConfiguration"
 	validatingWebhookConfigurationKind = "ValidatingWebhookConfiguration"
 	customResourceDefinitionKind       = "CustomResourceDefinition"
 )
 
-const (
-	// WebhookNamespaceName is the namespace used to deploy Cluster API webhooks.
-	WebhookNamespaceName = "capi-webhook-system"
-)
-
 // Components wraps a YAML file that defines the provider components
 // to be installed in a management cluster (CRD, Controller, RBAC etc.)
 // It is important to notice that clusterctl applies a set of processing steps to the “raw” component YAML read
@@ -313,6 +309,8 @@ func fixTargetNamespace(objs []unstructured.Unstructured, targetNamespace string
 			o.SetName(targetNamespace)
 		}
 
+		originalNamespace := o.GetNamespace()
+
 		// if the object is namespaced, set the namespace name
 		if util.IsResourceNamespaced(o.GetKind()) {
 			o.SetNamespace(targetNamespace)
@@ -325,6 +323,14 @@ func fixTargetNamespace(objs []unstructured.Unstructured, targetNamespace string
 				return nil, err
 			}
 		}
+
+		if o.GetKind() == certificateKind {
+			var err error
+			o, err = fixCertificate(o, originalNamespace, targetNamespace)
+			if err != nil {
+				return nil, err
+			}
+		}
 		objs[i] = o
 	}
 	return objs, nil
@@ -413,6 +419,7 @@ func fixValidatingWebhookNamespaceReferences(o unstructured.Unstructured, target
 	}
 	return o, errors.Errorf("failed to patch %s ValidatingWebhookConfiguration", version)
 }
+
 func fixCRDWebhookNamespaceReference(o unstructured.Unstructured, targetNamespace string) (unstructured.Unstructured, error) {
 	version := o.GroupVersionKind().Version
 	switch version {
@@ -439,6 +446,33 @@ func fixCRDWebhookNamespaceReference(o unstructured.Unstructured, targetNamespac
 	return o, errors.Errorf("failed to patch %s CustomResourceDefinition", version)
 }
 
+// fixCertificate fixes the dnsNames of cert-manager Certificates. The DNS names contain the dns names of the provider
+// services (including the namespace) and thus have to be modified to use the target namespace instead.
+func fixCertificate(o unstructured.Unstructured, originalNamespace, targetNamespace string) (unstructured.Unstructured, error) {
+	dnsNames, ok, err := unstructured.NestedStringSlice(o.UnstructuredContent(), "spec", "dnsNames")
+	if err != nil {
+		return o, errors.Wrapf(err, "failed to get .spec.dnsNames from Certificate %s/%s", o.GetNamespace(), o.GetName())
+	}
+	// Return if we don't find .spec.dnsNames.
+	if !ok {
+		return o, nil
+	}
+
+	// Iterate through dnsNames and adjust the namespace.
+	// The dnsNames slice usually looks like this:
+	// - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc
+	// - $(SERVICE_NAME).$(SERVICE_NAMESPACE).svc.cluster.local
+	for i, dnsName := range dnsNames {
+		dnsNames[i] = strings.Replace(dnsName, fmt.Sprintf(".%s.", originalNamespace), fmt.Sprintf(".%s.", targetNamespace), 1)
+	}
+
+	if err := unstructured.SetNestedStringSlice(o.UnstructuredContent(), dnsNames, "spec", "dnsNames"); err != nil {
+		return o, errors.Wrapf(err, "failed to set .spec.dnsNames to Certificate %s/%s", o.GetNamespace(), o.GetName())
+	}
+
+	return o, nil
+}
+
 // fixRBAC ensures all the ClusterRole and ClusterRoleBinding have the name prefixed with the namespace name and that
 // all the clusterRole/clusterRoleBinding namespaced subjects refers to targetNamespace.
 func fixRBAC(objs []unstructured.Unstructured, targetNamespace string) ([]unstructured.Unstructured, error) {
diff --git a/cmd/clusterctl/client/repository/components_test.go b/cmd/clusterctl/client/repository/components_test.go
index 50fc48a5f716..840e835acf10 100644
--- a/cmd/clusterctl/client/repository/components_test.go
+++ b/cmd/clusterctl/client/repository/components_test.go
@@ -523,6 +523,58 @@ func Test_fixTargetNamespace(t *testing.T) {
 				},
 			},
 		},
+		{
+			name: "fix cert-manager Certificate",
+			objs: []unstructured.Unstructured{
+				{
+					Object: map[string]interface{}{
+						"apiVersion": "cert-manager.io/v1",
+						"kind":       "Certificate",
+						"metadata": map[string]interface{}{
+							"name":      "capi-serving-cert",
+							"namespace": "capi-system",
+						},
+						"spec": map[string]interface{}{
+							"dnsNames": []interface{}{
+								"capi-webhook-service.capi-system.svc",
+								"capi-webhook-service.capi-system.svc.cluster.local",
+								"random-other-dns-name",
+							},
+							"issuerRef": map[string]interface{}{
+								"kind": "Issuer",
+								"name": "capi-selfsigned-issuer",
+							},
+							"secretName": "capi-webhook-service-cert",
+						},
+					},
+				},
+			},
+			targetNamespace: "bar",
+			want: []unstructured.Unstructured{
+				{
+					Object: map[string]interface{}{
+						"apiVersion": "cert-manager.io/v1",
+						"kind":       "Certificate",
+						"metadata": map[string]interface{}{
+							"name":      "capi-serving-cert",
+							"namespace": "bar",
+						},
+						"spec": map[string]interface{}{
+							"dnsNames": []interface{}{
+								"capi-webhook-service.bar.svc",
+								"capi-webhook-service.bar.svc.cluster.local",
+								"random-other-dns-name",
+							},
+							"issuerRef": map[string]interface{}{
+								"kind": "Issuer",
+								"name": "capi-selfsigned-issuer",
+							},
+							"secretName": "capi-webhook-service-cert",
+						},
+					},
+				},
+			},
+		},
 	}
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {