diff --git a/Makefile b/Makefile
index 38c9860ae75b..42cd0d8afb7c 100644
--- a/Makefile
+++ b/Makefile
@@ -50,8 +50,8 @@ hypershift:
 # deepcopy code and CRD manifest files.
 .PHONY: api
 api:
-	$(CONTROLLER_GEN) object:headerFile="hack/boilerplate.go.txt" paths="./..."
-	$(CONTROLLER_GEN) $(CRD_OPTIONS) paths="./..." output:crd:artifacts:config=cmd/install/assets/hypershift-operator
+	$(CONTROLLER_GEN) object:headerFile="hack/boilerplate.go.txt" paths="./api/..."
+	$(CONTROLLER_GEN) $(CRD_OPTIONS) paths="./api/..." output:crd:artifacts:config=cmd/install/assets/hypershift-operator
 
 # Run tests
 .PHONY: test
diff --git a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_externalinfraclusters.yaml b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_externalinfraclusters.yaml
index aae3000599a4..06dba7ed02c8 100644
--- a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_externalinfraclusters.yaml
+++ b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_externalinfraclusters.yaml
@@ -4,7 +4,7 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    controller-gen.kubebuilder.io/version: v0.3.0
+    controller-gen.kubebuilder.io/version: v0.5.0
   creationTimestamp: null
   name: externalinfraclusters.hypershift.openshift.io
 spec:
diff --git a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedclusters.yaml b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedclusters.yaml
index 22954e2f4345..9f2f0bbddb98 100644
--- a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedclusters.yaml
+++ b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedclusters.yaml
@@ -4,7 +4,7 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    controller-gen.kubebuilder.io/version: v0.3.0
+    controller-gen.kubebuilder.io/version: v0.5.0
   creationTimestamp: null
   name: hostedclusters.hypershift.openshift.io
 spec:
diff --git a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedcontrolplanes.yaml b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedcontrolplanes.yaml
index 9b57132ddb40..f79da875f167 100644
--- a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedcontrolplanes.yaml
+++ b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_hostedcontrolplanes.yaml
@@ -4,7 +4,7 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    controller-gen.kubebuilder.io/version: v0.3.0
+    controller-gen.kubebuilder.io/version: v0.5.0
   creationTimestamp: null
   name: hostedcontrolplanes.hypershift.openshift.io
 spec:
diff --git a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_nodepools.yaml b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_nodepools.yaml
index f153233b923f..66d17477007f 100644
--- a/cmd/install/assets/hypershift-operator/hypershift.openshift.io_nodepools.yaml
+++ b/cmd/install/assets/hypershift-operator/hypershift.openshift.io_nodepools.yaml
@@ -4,7 +4,7 @@ apiVersion: apiextensions.k8s.io/v1
 kind: CustomResourceDefinition
 metadata:
   annotations:
-    controller-gen.kubebuilder.io/version: v0.3.0
+    controller-gen.kubebuilder.io/version: v0.5.0
   creationTimestamp: null
   name: nodepools.hypershift.openshift.io
 spec: