diff --git a/pkg/cli/alpha/internal/generate.go b/pkg/cli/alpha/internal/generate.go
index c31f88bb158..bb410c79cb8 100644
--- a/pkg/cli/alpha/internal/generate.go
+++ b/pkg/cli/alpha/internal/generate.go
@@ -521,6 +521,11 @@ func getAPIResourceFlags(res resource.Resource) []string {
 		} else {
 			args = append(args, "--namespaced=false")
 		}
+		if res.API.GenerateApplyConfiguration {
+			args = append(args, "--generate-apply-configuration")
+		} else {
+			args = append(args, "--generate-apply-configuration=false")
+		}
 	}
 	if res.Controller {
 		args = append(args, "--controller")
diff --git a/pkg/model/resource/api.go b/pkg/model/resource/api.go
index 002205161ca..c346bc24198 100644
--- a/pkg/model/resource/api.go
+++ b/pkg/model/resource/api.go
@@ -27,6 +27,9 @@ type API struct {
 
 	// Namespaced is true if the API is namespaced.
 	Namespaced bool `json:"namespaced,omitempty"`
+
+	// GenerateApplyConfiguration indicates whether to generate applyconfiguration code for the resource.
+	GenerateApplyConfiguration bool `json:"generateApplyConfiguration,omitempty"`
 }
 
 // Validate checks that the API is valid.
@@ -65,6 +68,9 @@ func (api *API) Update(other *API) error {
 	// Update the namespace.
 	api.Namespaced = api.Namespaced || other.Namespaced
 
+	// Update the generate apply configuration flag.
+	api.GenerateApplyConfiguration = api.GenerateApplyConfiguration || other.GenerateApplyConfiguration
+
 	return nil
 }
 
diff --git a/pkg/model/resource/resource.go b/pkg/model/resource/resource.go
index 4c429b3642e..197bee268c0 100644
--- a/pkg/model/resource/resource.go
+++ b/pkg/model/resource/resource.go
@@ -140,6 +140,11 @@ func (r Resource) IsRegularPlural() bool {
 	return r.Plural == RegularPlural(r.Kind)
 }
 
+// HasApplyConfiguration returns true if the resource has applyconfiguration generation enabled.
+func (r Resource) HasApplyConfiguration() bool {
+	return r.API != nil && r.API.GenerateApplyConfiguration
+}
+
 // Copy returns a deep copy of the Resource that can be safely modified without affecting the original.
 func (r Resource) Copy() Resource {
 	// As this function doesn't use a pointer receiver, r is already a shallow copy.
diff --git a/pkg/plugins/golang/options.go b/pkg/plugins/golang/options.go
index 438d245ea11..8c73d091726 100644
--- a/pkg/plugins/golang/options.go
+++ b/pkg/plugins/golang/options.go
@@ -68,6 +68,9 @@ type Options struct {
 	// Namespaced is true if the resource should be namespaced.
 	Namespaced bool
 
+	// GenerateApplyConfiguration indicates whether to generate applyconfiguration code for the resource.
+	GenerateApplyConfiguration bool
+
 	// Flags that define which parts should be scaffolded
 	DoAPI        bool
 	DoController bool
@@ -95,8 +98,9 @@ func (opts Options) UpdateResource(res *resource.Resource, c config.Config) {
 		res.Path = resource.APIPackagePath(c.GetRepository(), res.Group, res.Version, c.IsMultiGroup())
 
 		res.API = &resource.API{
-			CRDVersion: "v1",
-			Namespaced: opts.Namespaced,
+			CRDVersion:                 "v1",
+			Namespaced:                 opts.Namespaced,
+			GenerateApplyConfiguration: opts.GenerateApplyConfiguration,
 		}
 	}
 
diff --git a/pkg/plugins/golang/v4/api.go b/pkg/plugins/golang/v4/api.go
index 3d49fb10966..4aad0995e3a 100644
--- a/pkg/plugins/golang/v4/api.go
+++ b/pkg/plugins/golang/v4/api.go
@@ -104,6 +104,7 @@ func (p *createAPISubcommand) BindFlags(fs *pflag.FlagSet) {
 		"if set, generate the resource without prompting the user")
 	p.resourceFlag = fs.Lookup("resource")
 	fs.BoolVar(&p.options.Namespaced, "namespaced", true, "resource is namespaced")
+	fs.BoolVar(&p.options.GenerateApplyConfiguration, "generate-apply-configuration", true, "if set, generate applyconfiguration code for the resource")
 
 	fs.BoolVar(&p.options.DoController, "controller", true,
 		"if set, generate the controller without prompting the user")
diff --git a/pkg/plugins/golang/v4/scaffolds/api.go b/pkg/plugins/golang/v4/scaffolds/api.go
index aa8c708417a..e4b088914f5 100644
--- a/pkg/plugins/golang/v4/scaffolds/api.go
+++ b/pkg/plugins/golang/v4/scaffolds/api.go
@@ -100,6 +100,7 @@ func (s *apiScaffolder) Scaffold() error {
 		if err := scaffold.Execute(
 			&api.Types{Force: s.force},
 			&api.Group{},
+			&api.Doc{},
 		); err != nil {
 			return fmt.Errorf("error scaffolding APIs: %w", err)
 		}
diff --git a/pkg/plugins/golang/v4/scaffolds/internal/templates/api/doc.go b/pkg/plugins/golang/v4/scaffolds/internal/templates/api/doc.go
new file mode 100644
index 00000000000..031976b0bfc
--- /dev/null
+++ b/pkg/plugins/golang/v4/scaffolds/internal/templates/api/doc.go
@@ -0,0 +1,59 @@
+/*
+Copyright 2022 The Kubernetes Authors.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package api
+
+import (
+	log "log/slog"
+	"path/filepath"
+
+	"sigs.k8s.io/kubebuilder/v4/pkg/machinery"
+)
+
+var _ machinery.Template = &Doc{}
+
+// Doc scaffolds the doc file that defines the groupName
+type Doc struct {
+	machinery.TemplateMixin
+	machinery.MultiGroupMixin
+	machinery.BoilerplateMixin
+	machinery.ResourceMixin
+}
+
+// SetTemplateDefaults implements machinery.Template
+func (f *Doc) SetTemplateDefaults() error {
+	if f.Path == "" {
+		if f.MultiGroup && f.Resource.Group != "" {
+			f.Path = filepath.Join("api", "%[group]", "%[version]", "doc.go")
+		} else {
+			f.Path = filepath.Join("api", "%[version]", "doc.go")
+		}
+	}
+
+	f.Path = f.Resource.Replacer().Replace(f.Path)
+	log.Info(f.Path)
+	f.TemplateBody = docTemplate
+
+	return nil
+}
+
+//nolint:lll
+const docTemplate = `{{ .Boilerplate }}
+
+// Package {{ .Resource.Version }} contains API Schema definitions for the {{ .Resource.Group }} {{ .Resource.Version }} API group.
+// +groupName={{ .Resource.QualifiedGroup }}
+package {{ .Resource.Version }}
+`
diff --git a/pkg/plugins/golang/v4/scaffolds/internal/templates/api/group.go b/pkg/plugins/golang/v4/scaffolds/internal/templates/api/group.go
index 817722b461b..612ebe35a94 100644
--- a/pkg/plugins/golang/v4/scaffolds/internal/templates/api/group.go
+++ b/pkg/plugins/golang/v4/scaffolds/internal/templates/api/group.go
@@ -55,7 +55,6 @@ const groupTemplate = `{{ .Boilerplate }}
 
 // Package {{ .Resource.Version }} contains API Schema definitions for the {{ .Resource.Group }} {{ .Resource.Version }} API group.
 // +kubebuilder:object:generate=true
-// +groupName={{ .Resource.QualifiedGroup }}
 package {{ .Resource.Version }}
 
 import (
@@ -67,8 +66,11 @@ var (
 	// GroupVersion is group version used to register these objects.
 	GroupVersion = schema.GroupVersion{Group: "{{ .Resource.QualifiedGroup }}", Version: "{{ .Resource.Version }}"}
 
+	// SchemeGroupVersion is necessary for applyconfiguration codegen.
+	SchemeGroupVersion = GroupVersion
+
 	// SchemeBuilder is used to add go types to the GroupVersionKind scheme.
-	SchemeBuilder = &scheme.Builder{GroupVersion: GroupVersion}
+	SchemeBuilder = &scheme.Builder{GroupVersion: SchemeGroupVersion}
 
 	// AddToScheme adds the types in this group-version to the given scheme.
 	AddToScheme = SchemeBuilder.AddToScheme
diff --git a/pkg/plugins/golang/v4/scaffolds/internal/templates/api/types.go b/pkg/plugins/golang/v4/scaffolds/internal/templates/api/types.go
index 6996047e875..65f5a147360 100644
--- a/pkg/plugins/golang/v4/scaffolds/internal/templates/api/types.go
+++ b/pkg/plugins/golang/v4/scaffolds/internal/templates/api/types.go
@@ -64,6 +64,11 @@ func (f *Types) SetTemplateDefaults() error {
 //nolint:lll
 const typesTemplate = `{{ .Boilerplate }}
 
+{{ if .Resource.HasApplyConfiguration }}
+// +kubebuilder:ac:generate=true
+{{ else }}
+// +kubebuilder:ac:generate=false
+{{ end }}
 package {{ .Resource.Version }}
 
 import (
@@ -116,6 +121,8 @@ type {{ .Resource.Kind }}Status struct {
 // +kubebuilder:resource:scope=Cluster
 {{- else if not .Resource.IsRegularPlural }}
 // +kubebuilder:resource:path={{ .Resource.Plural }}
+{{- else }}
+// +kubebuilder:resource
 {{- end }}
 
 // {{ .Resource.Kind }} is the Schema for the {{ .Resource.Plural }} API
diff --git a/pkg/plugins/golang/v4/scaffolds/internal/templates/makefile.go b/pkg/plugins/golang/v4/scaffolds/internal/templates/makefile.go
index 4ee5fbc7ff7..eb0b1bdf0fd 100644
--- a/pkg/plugins/golang/v4/scaffolds/internal/templates/makefile.go
+++ b/pkg/plugins/golang/v4/scaffolds/internal/templates/makefile.go
@@ -123,9 +123,9 @@ manifests: controller-gen ## Generate WebhookConfiguration, ClusterRole and Cust
 .PHONY: generate
 generate: controller-gen ## Generate code containing DeepCopy, DeepCopyInto, and DeepCopyObject method implementations.
 	{{ if .BoilerplatePath -}}
-	"$(CONTROLLER_GEN)" object:headerFile={{printf "%q" .BoilerplatePath}} paths="./..."
+	"$(CONTROLLER_GEN)" applyconfiguration:headerFile="hack/boilerplate.go.txt" object:headerFile={{printf "%q" .BoilerplatePath}} paths="./..."
 	{{- else -}}
-	"$(CONTROLLER_GEN)" object paths="./..."
+	"$(CONTROLLER_GEN)" applyconfiguration object paths="./..."
 	{{- end }}
 
 .PHONY: fmt