diff --git a/hack/charts/cluster-api-operator/templates/core.yaml b/hack/charts/cluster-api-operator/templates/core.yaml
index 260efb59..4235cd71 100644
--- a/hack/charts/cluster-api-operator/templates/core.yaml
+++ b/hack/charts/cluster-api-operator/templates/core.yaml
@@ -43,6 +43,15 @@ spec:
 {{- if $coreVersion }}
   version: {{ $coreVersion }}
 {{- end }}
+{{- if $.Values.manager }}
+  manager:
+{{- if $.Values.manager.featureGates.core }}
+    featureGates:
+    {{- range $key, $value := $.Values.manager.featureGates.core }}
+      {{ $key }}: {{ $value }}
+    {{- end }}
+{{- end }}
+{{- end }}
 {{- if $.Values.configSecret.name }}
   configSecret:
     name: {{ $.Values.configSecret.name }}
diff --git a/hack/charts/cluster-api-operator/templates/infra.yaml b/hack/charts/cluster-api-operator/templates/infra.yaml
index d7b46e71..5f813a22 100644
--- a/hack/charts/cluster-api-operator/templates/infra.yaml
+++ b/hack/charts/cluster-api-operator/templates/infra.yaml
@@ -46,10 +46,14 @@ spec:
 {{- end }}
 {{- if $.Values.manager }}
   manager:
-{{- if $.Values.manager.featureGates }}
-    featureGates:
+{{- if hasKey $.Values.manager.featureGates $infrastructureName }}
 {{- range $key, $value := $.Values.manager.featureGates }}
-      {{ $key }}: {{ $value }}
+  {{- if eq $key $infrastructureName }}
+    featureGates:
+    {{- range $k, $v := $value }}
+      {{ $k }}: {{ $v }}
+    {{- end }}
+  {{- end }}
 {{- end }}
 {{- end }}
 {{- end }}
diff --git a/test/e2e/helm_test.go b/test/e2e/helm_test.go
index 066ca938..9f109ab8 100644
--- a/test/e2e/helm_test.go
+++ b/test/e2e/helm_test.go
@@ -206,4 +206,27 @@ var _ = Describe("Create a proper set of manifests when using helm charts", func
 		Expect(err).ToNot(HaveOccurred())
 		Expect(manifests).To(Equal(string(expectedManifests)))
 	})
+	It("should deploy core and infra with feature gates enabled", func() {
+		manifests, err := helmChart.Run(map[string]string{
+			"configSecret.name":        "aws-variables",
+			"configSecret.namespace":   "default",
+			"infrastructure":           "aws:v2.4.0",
+			"addon":                    "helm:",
+			"image.manager.tag":        "v0.9.1",
+			"cert-manager.enabled":     "false",
+			"cert-manager.installCRDs": "false",
+			"core":                     "cluster-api:v1.6.2",
+			"manager.featureGates.core.ClusterTopology": "true",
+			"manager.featureGates.core.MachinePool":     "true",
+			"manager.featureGates.aws.ClusterTopology":  "true",
+			"manager.featureGates.aws.MachinePool":      "true",
+			"manager.featureGates.aws.EKSEnableIAM":     "true",
+			"manager.featureGates.aws.EKSAllowAddRoles": "true",
+		})
+		Expect(err).ToNot(HaveOccurred())
+		Expect(manifests).ToNot(BeEmpty())
+		expectedManifests, err := os.ReadFile(filepath.Join(customManifestsFolder, "feature-gates.yaml"))
+		Expect(err).ToNot(HaveOccurred())
+		Expect(manifests).To(Equal(string(expectedManifests)))
+	})
 })
diff --git a/test/e2e/resources/feature-gates.yaml b/test/e2e/resources/feature-gates.yaml
new file mode 100644
index 00000000..2bc1baa8
--- /dev/null
+++ b/test/e2e/resources/feature-gates.yaml
@@ -0,0 +1,123 @@
+---
+# Source: cluster-api-operator/templates/addon.yaml
+apiVersion: v1
+kind: Namespace
+metadata:
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "1"
+  name: helm-addon-system
+---
+# Source: cluster-api-operator/templates/core.yaml
+apiVersion: v1
+kind: Namespace
+metadata:
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "1"
+  name: capi-system
+---
+# Source: cluster-api-operator/templates/infra-conditions.yaml
+apiVersion: v1
+kind: Namespace
+metadata:
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "1"
+  name: capi-kubeadm-bootstrap-system
+---
+# Source: cluster-api-operator/templates/infra-conditions.yaml
+apiVersion: v1
+kind: Namespace
+metadata:
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "1"
+  name: capi-kubeadm-control-plane-system
+---
+# Source: cluster-api-operator/templates/infra.yaml
+apiVersion: v1
+kind: Namespace
+metadata:
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "1"
+  name: aws-infrastructure-system
+---
+# Source: cluster-api-operator/templates/addon.yaml
+apiVersion: operator.cluster.x-k8s.io/v1alpha2
+kind: AddonProvider
+metadata:
+  name: helm
+  namespace: helm-addon-system
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "2"
+---
+# Source: cluster-api-operator/templates/infra-conditions.yaml
+apiVersion: operator.cluster.x-k8s.io/v1alpha2
+kind: BootstrapProvider
+metadata:
+  name: kubeadm
+  namespace: capi-kubeadm-bootstrap-system
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "2"
+spec:
+  configSecret:
+    name: aws-variables
+    namespace: default
+---
+# Source: cluster-api-operator/templates/infra-conditions.yaml
+apiVersion: operator.cluster.x-k8s.io/v1alpha2
+kind: ControlPlaneProvider
+metadata:
+  name: kubeadm
+  namespace: capi-kubeadm-control-plane-system
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "2"
+spec:
+  configSecret:
+    name: aws-variables
+    namespace: default
+---
+# Source: cluster-api-operator/templates/core.yaml
+apiVersion: operator.cluster.x-k8s.io/v1alpha2
+kind: CoreProvider
+metadata:
+  name: cluster-api
+  namespace: capi-system
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "2"
+spec:
+  version: v1.6.2
+  manager:
+    featureGates:
+      ClusterTopology: true
+      MachinePool: true
+  configSecret:
+    name: aws-variables
+    namespace: default
+---
+# Source: cluster-api-operator/templates/infra.yaml
+apiVersion: operator.cluster.x-k8s.io/v1alpha2
+kind: InfrastructureProvider
+metadata:
+  name: aws
+  namespace: aws-infrastructure-system
+  annotations:
+    "helm.sh/hook": "post-install"
+    "helm.sh/hook-weight": "2"
+spec:
+  version: v2.4.0
+  manager:
+    featureGates:
+      ClusterTopology: true
+      EKSAllowAddRoles: true
+      EKSEnableIAM: true
+      MachinePool: true
+  configSecret:
+    name: aws-variables
+    namespace: default
\ No newline at end of file