diff --git a/generate_testdata.sh b/generate_testdata.sh
index f66b16df5d9..692d7b05528 100755
--- a/generate_testdata.sh
+++ b/generate_testdata.sh
@@ -98,7 +98,7 @@ scaffold_test_project() {
 
     $kb create api --group foo.policy --version v1 --kind HealthCheckPolicy --controller=true --resource=true --make=false
 
-    $kb create api --group apps --version v1 --kind Pod --controller=true --resource=false --make=false
+    $kb create api --group apps --version v1 --kind Deployment --controller=true --resource=false --make=false
 
     if [ $project == "project-v3-multigroup" ]; then
       $kb create api --version v1 --kind Lakers --controller=true --resource=true --make=false
diff --git a/pkg/model/file/funcmap.go b/pkg/model/file/funcmap.go
index 95d921c189a..a0a9432427b 100644
--- a/pkg/model/file/funcmap.go
+++ b/pkg/model/file/funcmap.go
@@ -26,12 +26,18 @@ import (
 // DefaultFuncMap returns the default template.FuncMap for rendering the template.
 func DefaultFuncMap() template.FuncMap {
 	return template.FuncMap{
-		"title":   strings.Title,
-		"lower":   strings.ToLower,
-		"hashFNV": hashFNV,
+		"title":      strings.Title,
+		"lower":      strings.ToLower,
+		"isEmptyStr": isEmptyString,
+		"hashFNV":    hashFNV,
 	}
 }
 
+// isEmptyString returns whether the string is empty
+func isEmptyString(s string) bool {
+	return s == ""
+}
+
 // hashFNV will generate a random string useful for generating a unique string
 func hashFNV(s string) (string, error) {
 	hasher := fnv.New32a()
diff --git a/pkg/model/resource/resource.go b/pkg/model/resource/resource.go
index 869b4a7e4d0..f5a36ba567c 100644
--- a/pkg/model/resource/resource.go
+++ b/pkg/model/resource/resource.go
@@ -155,8 +155,12 @@ func (r *Resource) Update(other Resource) error {
 		return fmt.Errorf("unable to update Resource with another with non-matching Plural")
 	}
 
-	if r.Path != other.Path {
-		return fmt.Errorf("unable to update Resource with another with non-matching Path")
+	if other.Path != "" && r.Path != other.Path {
+		if r.Path == "" {
+			r.Path = other.Path
+		} else {
+			return fmt.Errorf("unable to update Resource with another with non-matching Path")
+		}
 	}
 
 	// Update API.
diff --git a/pkg/plugins/golang/options.go b/pkg/plugins/golang/options.go
index ab2a2e0c96b..892217da7ca 100644
--- a/pkg/plugins/golang/options.go
+++ b/pkg/plugins/golang/options.go
@@ -137,7 +137,6 @@ func (opts Options) GVK() resource.GVK {
 func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	res := resource.Resource{
 		GVK:        opts.GVK(),
-		Path:       resource.APIPackagePath(c.GetRepository(), opts.Group, opts.Version, c.IsMultiGroup()),
 		Controller: opts.DoController,
 	}
 
@@ -149,6 +148,7 @@ func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	}
 
 	if opts.DoAPI {
+		res.Path = resource.APIPackagePath(c.GetRepository(), opts.Group, opts.Version, c.IsMultiGroup())
 		res.API = &resource.API{
 			CRDVersion: opts.CRDVersion,
 			Namespaced: opts.Namespaced,
@@ -159,6 +159,7 @@ func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	}
 
 	if opts.DoDefaulting || opts.DoValidation || opts.DoConversion {
+		res.Path = resource.APIPackagePath(c.GetRepository(), opts.Group, opts.Version, c.IsMultiGroup())
 		res.Webhooks = &resource.Webhooks{
 			WebhookVersion: opts.WebhookVersion,
 			Defaulting:     opts.DoDefaulting,
@@ -177,7 +178,9 @@ func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	//  - In any other case, default to                          => project resource
 	// TODO: need to support '--resource-pkg-path' flag for specifying resourcePath
 	if !opts.DoAPI {
-		if !c.HasResource(opts.GVK()) {
+		loadedRes, err := c.GetResource(opts.GVK())
+		alreadyHasAPI := err == nil && loadedRes.HasAPI()
+		if !alreadyHasAPI {
 			if domain, found := coreGroups[opts.Group]; found {
 				res.Domain = domain
 				res.Path = path.Join("k8s.io", "api", opts.Group, opts.Version)
diff --git a/pkg/plugins/golang/options_test.go b/pkg/plugins/golang/options_test.go
index 983313fb111..8faa101d975 100644
--- a/pkg/plugins/golang/options_test.go
+++ b/pkg/plugins/golang/options_test.go
@@ -62,6 +62,8 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -70,19 +72,36 @@ var _ = Describe("Options", func() {
 					Expect(resource.Domain).To(Equal(options.Domain))
 					Expect(resource.Version).To(Equal(options.Version))
 					Expect(resource.Kind).To(Equal(options.Kind))
-					if multiGroup {
-						Expect(resource.Path).To(Equal(
-							path.Join(cfg.GetRepository(), "apis", options.Group, options.Version)))
+					Expect(resource.API).NotTo(BeNil())
+					if options.DoAPI || options.DoDefaulting || options.DoValidation || options.DoConversion {
+						if multiGroup {
+							Expect(resource.Path).To(Equal(
+								path.Join(cfg.GetRepository(), "apis", options.Group, options.Version)))
+						} else {
+							Expect(resource.Path).To(Equal(path.Join(cfg.GetRepository(), "api", options.Version)))
+						}
 					} else {
-						Expect(resource.Path).To(Equal(path.Join(cfg.GetRepository(), "api", options.Version)))
+						// Core-resources have a path despite not having an API/Webhook but they are not tested here
+						Expect(resource.Path).To(Equal(""))
+					}
+					if options.DoAPI {
+						Expect(resource.API.CRDVersion).To(Equal(options.CRDVersion))
+						Expect(resource.API.Namespaced).To(Equal(options.Namespaced))
+						Expect(resource.API.IsEmpty()).To(BeFalse())
+					} else {
+						Expect(resource.API.IsEmpty()).To(BeTrue())
 					}
-					Expect(resource.API.CRDVersion).To(Equal(options.CRDVersion))
-					Expect(resource.API.Namespaced).To(Equal(options.Namespaced))
 					Expect(resource.Controller).To(Equal(options.DoController))
-					Expect(resource.Webhooks.WebhookVersion).To(Equal(options.WebhookVersion))
-					Expect(resource.Webhooks.Defaulting).To(Equal(options.DoDefaulting))
-					Expect(resource.Webhooks.Validation).To(Equal(options.DoValidation))
-					Expect(resource.Webhooks.Conversion).To(Equal(options.DoConversion))
+					Expect(resource.Webhooks).NotTo(BeNil())
+					if options.DoDefaulting || options.DoValidation || options.DoConversion {
+						Expect(resource.Webhooks.WebhookVersion).To(Equal(options.WebhookVersion))
+						Expect(resource.Webhooks.Defaulting).To(Equal(options.DoDefaulting))
+						Expect(resource.Webhooks.Validation).To(Equal(options.DoValidation))
+						Expect(resource.Webhooks.Conversion).To(Equal(options.DoConversion))
+						Expect(resource.Webhooks.IsEmpty()).To(BeFalse())
+					} else {
+						Expect(resource.Webhooks.IsEmpty()).To(BeTrue())
+					}
 					Expect(resource.QualifiedGroup()).To(Equal(options.Group + "." + options.Domain))
 					Expect(resource.PackageName()).To(Equal(options.Group))
 					Expect(resource.ImportAlias()).To(Equal(options.Group + options.Version))
@@ -130,6 +149,8 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -150,6 +171,8 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -168,12 +191,15 @@ var _ = Describe("Options", func() {
 					Domain:  "test.io",
 					Version: "v1",
 					Kind:    "FirstMate",
+					DoAPI:   true, // Scaffold the API so that the path is saved
 				}
 				Expect(options.Validate()).To(Succeed())
 
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -201,6 +227,8 @@ var _ = Describe("Options", func() {
 			for _, multiGroup := range []bool{false, true} {
 				if multiGroup {
 					Expect(cfg.SetMultiGroup()).To(Succeed())
+				} else {
+					Expect(cfg.ClearMultiGroup()).To(Succeed())
 				}
 
 				resource := options.NewResource(cfg)
@@ -222,12 +250,15 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
 					Expect(resource.Validate()).To(Succeed())
 					Expect(resource.Path).To(Equal(path.Join("k8s.io", "api", options.Group, options.Version)))
-					Expect(resource.API.CRDVersion).To(Equal(""))
+					Expect(resource.API).NotTo(BeNil())
+					Expect(resource.API.IsEmpty()).To(BeTrue())
 					Expect(resource.QualifiedGroup()).To(Equal(qualified))
 				}
 			},
@@ -242,12 +273,15 @@ var _ = Describe("Options", func() {
 				Domain:  "test.io",
 				Version: "v1",
 				Kind:    "FirstMate",
+				DoAPI:   true, // Scaffold the API so that the path is saved
 			}
 			Expect(options.Validate()).To(Succeed())
 
 			for _, multiGroup := range []bool{false, true} {
 				if multiGroup {
 					Expect(cfg.SetMultiGroup()).To(Succeed())
+				} else {
+					Expect(cfg.ClearMultiGroup()).To(Succeed())
 				}
 
 				resource := options.NewResource(cfg)
diff --git a/pkg/plugins/golang/v2/api.go b/pkg/plugins/golang/v2/api.go
index 0c224a07d4a..bdca3497512 100644
--- a/pkg/plugins/golang/v2/api.go
+++ b/pkg/plugins/golang/v2/api.go
@@ -154,9 +154,9 @@ func (p *createAPISubcommand) Validate() error {
 	}
 
 	// In case we want to scaffold a resource API we need to do some checks
-	if p.resource.HasAPI() {
-		// Check that resource doesn't exist or flag force was set
-		if !p.force && p.config.HasResource(p.resource.GVK) {
+	if p.options.DoAPI {
+		// Check that resource doesn't have the API scaffolded or flag force was set
+		if res, err := p.config.GetResource(p.resource.GVK); err == nil && res.HasAPI() && !p.force {
 			return errors.New("API resource already exists")
 		}
 
diff --git a/pkg/plugins/golang/v2/options.go b/pkg/plugins/golang/v2/options.go
index 4b3613fe295..52f4410b838 100644
--- a/pkg/plugins/golang/v2/options.go
+++ b/pkg/plugins/golang/v2/options.go
@@ -22,6 +22,7 @@ import (
 	"strings"
 
 	newconfig "sigs.k8s.io/kubebuilder/v3/pkg/config"
+	cfgv2 "sigs.k8s.io/kubebuilder/v3/pkg/config/v2"
 	"sigs.k8s.io/kubebuilder/v3/pkg/model/resource"
 )
 
@@ -137,7 +138,6 @@ func (opts Options) GVK() resource.GVK {
 func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	res := resource.Resource{
 		GVK:        opts.GVK(),
-		Path:       resource.APIPackagePath(c.GetRepository(), opts.Group, opts.Version, c.IsMultiGroup()),
 		Controller: opts.DoController,
 	}
 
@@ -149,6 +149,7 @@ func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	}
 
 	if opts.DoAPI {
+		res.Path = resource.APIPackagePath(c.GetRepository(), opts.Group, opts.Version, c.IsMultiGroup())
 		res.API = &resource.API{
 			CRDVersion: opts.CRDVersion,
 			Namespaced: opts.Namespaced,
@@ -159,6 +160,7 @@ func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	}
 
 	if opts.DoDefaulting || opts.DoValidation || opts.DoConversion {
+		res.Path = resource.APIPackagePath(c.GetRepository(), opts.Group, opts.Version, c.IsMultiGroup())
 		res.Webhooks = &resource.Webhooks{
 			WebhookVersion: opts.WebhookVersion,
 			Defaulting:     opts.DoDefaulting,
@@ -177,7 +179,14 @@ func (opts Options) NewResource(c newconfig.Config) resource.Resource {
 	//  - In any other case, default to                          => project resource
 	// TODO: need to support '--resource-pkg-path' flag for specifying resourcePath
 	if !opts.DoAPI {
-		if !c.HasResource(opts.GVK()) {
+		var alreadyHasAPI bool
+		if c.GetVersion().Compare(cfgv2.Version) == 0 {
+			alreadyHasAPI = c.HasResource(opts.GVK())
+		} else {
+			loadedRes, err := c.GetResource(opts.GVK())
+			alreadyHasAPI = err == nil && loadedRes.HasAPI()
+		}
+		if !alreadyHasAPI {
 			if domain, found := coreGroups[opts.Group]; found {
 				res.Domain = domain
 				res.Path = path.Join("k8s.io", "api", opts.Group, opts.Version)
diff --git a/pkg/plugins/golang/v2/options_test.go b/pkg/plugins/golang/v2/options_test.go
index e4997e684a7..692a262e5ca 100644
--- a/pkg/plugins/golang/v2/options_test.go
+++ b/pkg/plugins/golang/v2/options_test.go
@@ -61,6 +61,8 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -69,19 +71,36 @@ var _ = Describe("Options", func() {
 					Expect(resource.Domain).To(Equal(options.Domain))
 					Expect(resource.Version).To(Equal(options.Version))
 					Expect(resource.Kind).To(Equal(options.Kind))
-					if multiGroup {
-						Expect(resource.Path).To(Equal(
-							path.Join(cfg.GetRepository(), "apis", options.Group, options.Version)))
+					Expect(resource.API).NotTo(BeNil())
+					if options.DoAPI || options.DoDefaulting || options.DoValidation || options.DoConversion {
+						if multiGroup {
+							Expect(resource.Path).To(Equal(
+								path.Join(cfg.GetRepository(), "apis", options.Group, options.Version)))
+						} else {
+							Expect(resource.Path).To(Equal(path.Join(cfg.GetRepository(), "api", options.Version)))
+						}
 					} else {
-						Expect(resource.Path).To(Equal(path.Join(cfg.GetRepository(), "api", options.Version)))
+						// Core-resources have a path despite not having an API/Webhook but they are not tested here
+						Expect(resource.Path).To(Equal(""))
+					}
+					if options.DoAPI {
+						Expect(resource.API.CRDVersion).To(Equal(options.CRDVersion))
+						Expect(resource.API.Namespaced).To(Equal(options.Namespaced))
+						Expect(resource.API.IsEmpty()).To(BeFalse())
+					} else {
+						Expect(resource.API.IsEmpty()).To(BeTrue())
 					}
-					Expect(resource.API.CRDVersion).To(Equal(options.CRDVersion))
-					Expect(resource.API.Namespaced).To(Equal(options.Namespaced))
 					Expect(resource.Controller).To(Equal(options.DoController))
-					Expect(resource.Webhooks.WebhookVersion).To(Equal(options.WebhookVersion))
-					Expect(resource.Webhooks.Defaulting).To(Equal(options.DoDefaulting))
-					Expect(resource.Webhooks.Validation).To(Equal(options.DoValidation))
-					Expect(resource.Webhooks.Conversion).To(Equal(options.DoConversion))
+					Expect(resource.Webhooks).NotTo(BeNil())
+					if options.DoDefaulting || options.DoValidation || options.DoConversion {
+						Expect(resource.Webhooks.WebhookVersion).To(Equal(options.WebhookVersion))
+						Expect(resource.Webhooks.Defaulting).To(Equal(options.DoDefaulting))
+						Expect(resource.Webhooks.Validation).To(Equal(options.DoValidation))
+						Expect(resource.Webhooks.Conversion).To(Equal(options.DoConversion))
+						Expect(resource.Webhooks.IsEmpty()).To(BeFalse())
+					} else {
+						Expect(resource.Webhooks.IsEmpty()).To(BeTrue())
+					}
 					Expect(resource.QualifiedGroup()).To(Equal(options.Group + "." + options.Domain))
 					Expect(resource.PackageName()).To(Equal(options.Group))
 					Expect(resource.ImportAlias()).To(Equal(options.Group + options.Version))
@@ -129,6 +148,8 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -149,6 +170,8 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -167,12 +190,15 @@ var _ = Describe("Options", func() {
 					Domain:  "test.io",
 					Version: "v1",
 					Kind:    "FirstMate",
+					DoAPI:   true, // Scaffold the API so that the path is saved
 				}
 				Expect(options.Validate()).To(Succeed())
 
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
@@ -200,6 +226,8 @@ var _ = Describe("Options", func() {
 			for _, multiGroup := range []bool{false, true} {
 				if multiGroup {
 					Expect(cfg.SetMultiGroup()).To(Succeed())
+				} else {
+					Expect(cfg.ClearMultiGroup()).To(Succeed())
 				}
 
 				resource := options.NewResource(cfg)
@@ -221,12 +249,15 @@ var _ = Describe("Options", func() {
 				for _, multiGroup := range []bool{false, true} {
 					if multiGroup {
 						Expect(cfg.SetMultiGroup()).To(Succeed())
+					} else {
+						Expect(cfg.ClearMultiGroup()).To(Succeed())
 					}
 
 					resource := options.NewResource(cfg)
 					Expect(resource.Validate()).To(Succeed())
 					Expect(resource.Path).To(Equal(path.Join("k8s.io", "api", options.Group, options.Version)))
-					Expect(resource.API.CRDVersion).To(Equal(""))
+					Expect(resource.API).NotTo(BeNil())
+					Expect(resource.API.IsEmpty()).To(BeTrue())
 					Expect(resource.QualifiedGroup()).To(Equal(qualified))
 				}
 			},
diff --git a/pkg/plugins/golang/v2/scaffolds/api.go b/pkg/plugins/golang/v2/scaffolds/api.go
index e4abc4d9ae6..353aac0e5f0 100644
--- a/pkg/plugins/golang/v2/scaffolds/api.go
+++ b/pkg/plugins/golang/v2/scaffolds/api.go
@@ -20,6 +20,7 @@ import (
 	"fmt"
 
 	"sigs.k8s.io/kubebuilder/v3/pkg/config"
+	cfgv2 "sigs.k8s.io/kubebuilder/v3/pkg/config/v2"
 	"sigs.k8s.io/kubebuilder/v3/pkg/model"
 	"sigs.k8s.io/kubebuilder/v3/pkg/model/resource"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v2/scaffolds/internal/templates"
@@ -89,11 +90,19 @@ func (s *apiScaffolder) scaffold() error {
 	doAPI := s.resource.HasAPI()
 	doController := s.resource.HasController()
 
-	if doAPI {
-
+	// Project version v2 only tracked GVK triplets of each resource.
+	// As they were only tracked when the API was scaffolded, the presence of a
+	// resource in the config file was used in webhook creation to verify that
+	// the API had been scaffolded previously. From project version v3 onwards
+	// this information is stored in the API field of the resource, so we can
+	// update the resources except for project version 2 when no API was scaffolded.
+	if doAPI || s.config.GetVersion().Compare(cfgv2.Version) == 1 {
 		if err := s.config.UpdateResource(s.resource); err != nil {
 			return fmt.Errorf("error updating resource: %w", err)
 		}
+	}
+
+	if doAPI {
 
 		if err := machinery.NewScaffold(s.plugins...).Execute(
 			s.newUniverse(),
diff --git a/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller.go b/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller.go
index b338e3b151f..ee059001455 100644
--- a/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller.go
+++ b/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller.go
@@ -72,7 +72,7 @@ import (
 	"k8s.io/apimachinery/pkg/runtime"
 	ctrl "sigs.k8s.io/controller-runtime"
 	"sigs.k8s.io/controller-runtime/pkg/client"
-	{{ if .Resource.HasAPI -}}
+	{{ if not (isEmptyStr .Resource.Path) -}}
 	{{ .Resource.ImportAlias }} "{{ .Resource.Path }}"
 	{{- end }}
 )
@@ -108,7 +108,7 @@ func (r *{{ .Resource.Kind }}Reconciler) Reconcile(req ctrl.Request) (ctrl.Resul
 // SetupWithManager sets up the controller with the Manager.
 func (r *{{ .Resource.Kind }}Reconciler) SetupWithManager(mgr ctrl.Manager) error {
 	return ctrl.NewControllerManagedBy(mgr).
-		{{ if .Resource.HasAPI -}}
+		{{ if not (isEmptyStr .Resource.Path) -}}
 		For(&{{ .Resource.ImportAlias }}.{{ .Resource.Kind }}{}).
 		{{- else -}}
 		// Uncomment the following line adding a pointer to an instance of the controlled resource as an argument
diff --git a/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller_suitetest.go b/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller_suitetest.go
index 34e1b418aa9..61bd1d584d7 100644
--- a/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller_suitetest.go
+++ b/pkg/plugins/golang/v2/scaffolds/internal/templates/controllers/controller_suitetest.go
@@ -98,13 +98,13 @@ func (f *SuiteTest) GetCodeFragments() file.CodeFragmentsMap {
 
 	// Generate import code fragments
 	imports := make([]string, 0)
-	if f.Resource.HasAPI() {
+	if f.Resource.Path != "" {
 		imports = append(imports, fmt.Sprintf(apiImportCodeFragment, f.Resource.ImportAlias(), f.Resource.Path))
 	}
 
 	// Generate add scheme code fragments
 	addScheme := make([]string, 0)
-	if f.Resource.HasAPI() {
+	if f.Resource.Path != "" {
 		addScheme = append(addScheme, fmt.Sprintf(addschemeCodeFragment, f.Resource.ImportAlias()))
 	}
 
diff --git a/pkg/plugins/golang/v2/webhook.go b/pkg/plugins/golang/v2/webhook.go
index 2c4b2f8bb7e..735c48c68df 100644
--- a/pkg/plugins/golang/v2/webhook.go
+++ b/pkg/plugins/golang/v2/webhook.go
@@ -24,6 +24,7 @@ import (
 	"github.com/spf13/pflag"
 
 	newconfig "sigs.k8s.io/kubebuilder/v3/pkg/config"
+	cfgv2 "sigs.k8s.io/kubebuilder/v3/pkg/config/v2"
 	"sigs.k8s.io/kubebuilder/v3/pkg/model/resource"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugin"
 	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang/v2/scaffolds"
@@ -104,8 +105,16 @@ func (p *createWebhookSubcommand) Validate() error {
 	}
 
 	// check if resource exist to create webhook
-	if !p.config.HasResource(p.resource.GVK) {
-		return fmt.Errorf("%s create webhook requires a previously created API ", p.commandName)
+	if p.config.GetVersion().Compare(cfgv2.Version) == 0 {
+		if !p.config.HasResource(p.resource.GVK) {
+			return fmt.Errorf("%s create webhook requires a previously created API ", p.commandName)
+		}
+	} else {
+		if r, err := p.config.GetResource(p.resource.GVK); err != nil {
+			return fmt.Errorf("%s create webhook requires a previously created API ", p.commandName)
+		} else if r.Webhooks != nil && !r.Webhooks.IsEmpty() {
+			return fmt.Errorf("webhook resource already exists")
+		}
 	}
 
 	return nil
diff --git a/pkg/plugins/golang/v3/api.go b/pkg/plugins/golang/v3/api.go
index 98a6462e40b..f71bc7e5e4f 100644
--- a/pkg/plugins/golang/v3/api.go
+++ b/pkg/plugins/golang/v3/api.go
@@ -176,8 +176,8 @@ func (p *createAPISubcommand) Validate() error {
 	}
 
 	// In case we want to scaffold a resource API we need to do some checks
-	if p.resource.HasAPI() {
-		// Check that resource doesn't exist or flag force was set
+	if p.options.DoAPI {
+		// Check that resource doesn't have the API scaffolded or flag force was set
 		if res, err := p.config.GetResource(p.resource.GVK); err == nil && res.HasAPI() && !p.force {
 			return errors.New("API resource already exists")
 		}
diff --git a/pkg/plugins/golang/v3/scaffolds/api.go b/pkg/plugins/golang/v3/scaffolds/api.go
index 0265d705b60..1d9698cafc3 100644
--- a/pkg/plugins/golang/v3/scaffolds/api.go
+++ b/pkg/plugins/golang/v3/scaffolds/api.go
@@ -86,11 +86,11 @@ func (s *apiScaffolder) scaffold() error {
 	doAPI := s.resource.HasAPI()
 	doController := s.resource.HasController()
 
-	if doAPI {
+	if err := s.config.UpdateResource(s.resource); err != nil {
+		return fmt.Errorf("error updating resource: %w", err)
+	}
 
-		if err := s.config.UpdateResource(s.resource); err != nil {
-			return fmt.Errorf("error updating resource: %w", err)
-		}
+	if doAPI {
 
 		if err := machinery.NewScaffold(s.plugins...).Execute(
 			s.newUniverse(),
diff --git a/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller.go b/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller.go
index a70eed4714d..779edb04b45 100644
--- a/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller.go
+++ b/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller.go
@@ -72,7 +72,7 @@ import (
 	"k8s.io/apimachinery/pkg/runtime"
 	ctrl "sigs.k8s.io/controller-runtime"
 	"sigs.k8s.io/controller-runtime/pkg/client"
-	{{ if .Resource.HasAPI -}}
+	{{ if not (isEmptyStr .Resource.Path) -}}
 	{{ .Resource.ImportAlias }} "{{ .Resource.Path }}"
 	{{- end }}
 )
@@ -108,7 +108,7 @@ func (r *{{ .Resource.Kind }}Reconciler) Reconcile(ctx context.Context, req ctrl
 // SetupWithManager sets up the controller with the Manager.
 func (r *{{ .Resource.Kind }}Reconciler) SetupWithManager(mgr ctrl.Manager) error {
 	return ctrl.NewControllerManagedBy(mgr).
-		{{ if .Resource.HasAPI -}}
+		{{ if not (isEmptyStr .Resource.Path) -}}
 		For(&{{ .Resource.ImportAlias }}.{{ .Resource.Kind }}{}).
 		{{- else -}}
 		// Uncomment the following line adding a pointer to an instance of the controlled resource as an argument
diff --git a/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller_suitetest.go b/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller_suitetest.go
index d8159a93c3e..d6e6ac95af5 100644
--- a/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller_suitetest.go
+++ b/pkg/plugins/golang/v3/scaffolds/internal/templates/controllers/controller_suitetest.go
@@ -98,13 +98,13 @@ func (f *SuiteTest) GetCodeFragments() file.CodeFragmentsMap {
 
 	// Generate import code fragments
 	imports := make([]string, 0)
-	if f.Resource.HasAPI() {
+	if f.Resource.Path != "" {
 		imports = append(imports, fmt.Sprintf(apiImportCodeFragment, f.Resource.ImportAlias(), f.Resource.Path))
 	}
 
 	// Generate add scheme code fragments
 	addScheme := make([]string, 0)
-	if f.Resource.HasAPI() {
+	if f.Resource.Path != "" {
 		addScheme = append(addScheme, fmt.Sprintf(addschemeCodeFragment, f.Resource.ImportAlias()))
 	}
 
diff --git a/pkg/plugins/golang/v3/webhook.go b/pkg/plugins/golang/v3/webhook.go
index 0139225b878..7c81b017fae 100644
--- a/pkg/plugins/golang/v3/webhook.go
+++ b/pkg/plugins/golang/v3/webhook.go
@@ -17,7 +17,6 @@ limitations under the License.
 package v3
 
 import (
-	"errors"
 	"fmt"
 	"io/ioutil"
 	"path/filepath"
@@ -119,7 +118,7 @@ func (p *createWebhookSubcommand) Validate() error {
 	if r, err := p.config.GetResource(p.resource.GVK); err != nil {
 		return fmt.Errorf("%s create webhook requires a previously created API ", p.commandName)
 	} else if r.Webhooks != nil && !r.Webhooks.IsEmpty() && !p.force {
-		return errors.New("webhook resource already exists")
+		return fmt.Errorf("webhook resource already exists")
 	}
 
 	if !p.config.IsWebhookVersionCompatible(p.resource.Webhooks.WebhookVersion) {
diff --git a/testdata/project-v2-multigroup/config/rbac/role.yaml b/testdata/project-v2-multigroup/config/rbac/role.yaml
index aef6d389cee..7ae49be3caa 100644
--- a/testdata/project-v2-multigroup/config/rbac/role.yaml
+++ b/testdata/project-v2-multigroup/config/rbac/role.yaml
@@ -9,7 +9,7 @@ rules:
 - apiGroups:
   - apps
   resources:
-  - pods
+  - deployments
   verbs:
   - create
   - delete
@@ -21,7 +21,7 @@ rules:
 - apiGroups:
   - apps
   resources:
-  - pods/status
+  - deployments/status
   verbs:
   - get
   - patch
diff --git a/testdata/project-v2-multigroup/controllers/apps/pod_controller.go b/testdata/project-v2-multigroup/controllers/apps/deployment_controller.go
similarity index 70%
rename from testdata/project-v2-multigroup/controllers/apps/pod_controller.go
rename to testdata/project-v2-multigroup/controllers/apps/deployment_controller.go
index 7cd866d048e..cf176817191 100644
--- a/testdata/project-v2-multigroup/controllers/apps/pod_controller.go
+++ b/testdata/project-v2-multigroup/controllers/apps/deployment_controller.go
@@ -20,33 +20,34 @@ import (
 	"context"
 
 	"github.com/go-logr/logr"
+	appsv1 "k8s.io/api/apps/v1"
 	"k8s.io/apimachinery/pkg/runtime"
 	ctrl "sigs.k8s.io/controller-runtime"
 	"sigs.k8s.io/controller-runtime/pkg/client"
 )
 
-// PodReconciler reconciles a Pod object
-type PodReconciler struct {
+// DeploymentReconciler reconciles a Deployment object
+type DeploymentReconciler struct {
 	client.Client
 	Log    logr.Logger
 	Scheme *runtime.Scheme
 }
 
-//+kubebuilder:rbac:groups=apps,resources=pods,verbs=get;list;watch;create;update;patch;delete
-//+kubebuilder:rbac:groups=apps,resources=pods/status,verbs=get;update;patch
+//+kubebuilder:rbac:groups=apps,resources=deployments,verbs=get;list;watch;create;update;patch;delete
+//+kubebuilder:rbac:groups=apps,resources=deployments/status,verbs=get;update;patch
 
 // Reconcile is part of the main kubernetes reconciliation loop which aims to
 // move the current state of the cluster closer to the desired state.
 // TODO(user): Modify the Reconcile function to compare the state specified by
-// the Pod object against the actual cluster state, and then
+// the Deployment object against the actual cluster state, and then
 // perform operations to make the cluster state reflect the state specified by
 // the user.
 //
 // For more details, check Reconcile and its Result here:
 // - https://pkg.go.dev/sigs.k8s.io/controller-runtime@v0.6.4/pkg/reconcile
-func (r *PodReconciler) Reconcile(req ctrl.Request) (ctrl.Result, error) {
+func (r *DeploymentReconciler) Reconcile(req ctrl.Request) (ctrl.Result, error) {
 	_ = context.Background()
-	_ = r.Log.WithValues("pod", req.NamespacedName)
+	_ = r.Log.WithValues("deployment", req.NamespacedName)
 
 	// your logic here
 
@@ -54,9 +55,8 @@ func (r *PodReconciler) Reconcile(req ctrl.Request) (ctrl.Result, error) {
 }
 
 // SetupWithManager sets up the controller with the Manager.
-func (r *PodReconciler) SetupWithManager(mgr ctrl.Manager) error {
+func (r *DeploymentReconciler) SetupWithManager(mgr ctrl.Manager) error {
 	return ctrl.NewControllerManagedBy(mgr).
-		// Uncomment the following line adding a pointer to an instance of the controlled resource as an argument
-		// For().
+		For(&appsv1.Deployment{}).
 		Complete(r)
 }
diff --git a/testdata/project-v2-multigroup/controllers/apps/suite_test.go b/testdata/project-v2-multigroup/controllers/apps/suite_test.go
index d4431b5013f..9c3d92e900b 100644
--- a/testdata/project-v2-multigroup/controllers/apps/suite_test.go
+++ b/testdata/project-v2-multigroup/controllers/apps/suite_test.go
@@ -22,6 +22,7 @@ import (
 
 	. "github.com/onsi/ginkgo"
 	. "github.com/onsi/gomega"
+	appsv1 "k8s.io/api/apps/v1"
 	"k8s.io/client-go/kubernetes/scheme"
 	"k8s.io/client-go/rest"
 	"sigs.k8s.io/controller-runtime/pkg/client"
@@ -60,6 +61,9 @@ var _ = BeforeSuite(func(done Done) {
 	Expect(err).ToNot(HaveOccurred())
 	Expect(cfg).ToNot(BeNil())
 
+	err = appsv1.AddToScheme(scheme.Scheme)
+	Expect(err).NotTo(HaveOccurred())
+
 	//+kubebuilder:scaffold:scheme
 
 	k8sClient, err = client.New(cfg, client.Options{Scheme: scheme.Scheme})
diff --git a/testdata/project-v2-multigroup/go.mod b/testdata/project-v2-multigroup/go.mod
index 2aeef58e0be..d0ffad76e06 100644
--- a/testdata/project-v2-multigroup/go.mod
+++ b/testdata/project-v2-multigroup/go.mod
@@ -6,6 +6,7 @@ require (
 	github.com/go-logr/logr v0.1.0
 	github.com/onsi/ginkgo v1.12.1
 	github.com/onsi/gomega v1.10.1
+	k8s.io/api v0.18.6
 	k8s.io/apimachinery v0.18.6
 	k8s.io/client-go v0.18.6
 	sigs.k8s.io/controller-runtime v0.6.4
diff --git a/testdata/project-v2-multigroup/main.go b/testdata/project-v2-multigroup/main.go
index 60aead1c253..9d8addc71ec 100644
--- a/testdata/project-v2-multigroup/main.go
+++ b/testdata/project-v2-multigroup/main.go
@@ -155,12 +155,12 @@ func main() {
 		setupLog.Error(err, "unable to create controller", "controller", "HealthCheckPolicy")
 		os.Exit(1)
 	}
-	if err = (&appscontroller.PodReconciler{
+	if err = (&appscontroller.DeploymentReconciler{
 		Client: mgr.GetClient(),
-		Log:    ctrl.Log.WithName("controllers").WithName("Pod"),
+		Log:    ctrl.Log.WithName("controllers").WithName("Deployment"),
 		Scheme: mgr.GetScheme(),
 	}).SetupWithManager(mgr); err != nil {
-		setupLog.Error(err, "unable to create controller", "controller", "Pod")
+		setupLog.Error(err, "unable to create controller", "controller", "Deployment")
 		os.Exit(1)
 	}
 	//+kubebuilder:scaffold:builder
diff --git a/testdata/project-v3-config/PROJECT b/testdata/project-v3-config/PROJECT
index 144702d87c3..804ab898289 100644
--- a/testdata/project-v3-config/PROJECT
+++ b/testdata/project-v3-config/PROJECT
@@ -40,4 +40,9 @@ resources:
   webhooks:
     defaulting: true
     webhookVersion: v1
+- controller: true
+  domain: testproject.org
+  group: crew
+  kind: Laker
+  version: v1
 version: "3"
diff --git a/testdata/project-v3-multigroup/PROJECT b/testdata/project-v3-multigroup/PROJECT
index 30a6a0ddfa7..4d23fb47636 100644
--- a/testdata/project-v3-multigroup/PROJECT
+++ b/testdata/project-v3-multigroup/PROJECT
@@ -78,6 +78,11 @@ resources:
   kind: HealthCheckPolicy
   path: sigs.k8s.io/kubebuilder/testdata/project-v3-multigroup/apis/foo.policy/v1
   version: v1
+- controller: true
+  group: apps
+  kind: Deployment
+  path: k8s.io/api/apps/v1
+  version: v1
 - api:
     crdVersion: v1
     namespaced: true
diff --git a/testdata/project-v3-multigroup/config/rbac/role.yaml b/testdata/project-v3-multigroup/config/rbac/role.yaml
index cd19ad8560a..5009fea150c 100644
--- a/testdata/project-v3-multigroup/config/rbac/role.yaml
+++ b/testdata/project-v3-multigroup/config/rbac/role.yaml
@@ -9,7 +9,7 @@ rules:
 - apiGroups:
   - apps
   resources:
-  - pods
+  - deployments
   verbs:
   - create
   - delete
@@ -21,13 +21,13 @@ rules:
 - apiGroups:
   - apps
   resources:
-  - pods/finalizers
+  - deployments/finalizers
   verbs:
   - update
 - apiGroups:
   - apps
   resources:
-  - pods/status
+  - deployments/status
   verbs:
   - get
   - patch
diff --git a/testdata/project-v3-multigroup/controllers/apps/pod_controller.go b/testdata/project-v3-multigroup/controllers/apps/deployment_controller.go
similarity index 66%
rename from testdata/project-v3-multigroup/controllers/apps/pod_controller.go
rename to testdata/project-v3-multigroup/controllers/apps/deployment_controller.go
index 8bfb4ed0dea..a18548c0177 100644
--- a/testdata/project-v3-multigroup/controllers/apps/pod_controller.go
+++ b/testdata/project-v3-multigroup/controllers/apps/deployment_controller.go
@@ -20,33 +20,34 @@ import (
 	"context"
 
 	"github.com/go-logr/logr"
+	appsv1 "k8s.io/api/apps/v1"
 	"k8s.io/apimachinery/pkg/runtime"
 	ctrl "sigs.k8s.io/controller-runtime"
 	"sigs.k8s.io/controller-runtime/pkg/client"
 )
 
-// PodReconciler reconciles a Pod object
-type PodReconciler struct {
+// DeploymentReconciler reconciles a Deployment object
+type DeploymentReconciler struct {
 	client.Client
 	Log    logr.Logger
 	Scheme *runtime.Scheme
 }
 
-//+kubebuilder:rbac:groups=apps,resources=pods,verbs=get;list;watch;create;update;patch;delete
-//+kubebuilder:rbac:groups=apps,resources=pods/status,verbs=get;update;patch
-//+kubebuilder:rbac:groups=apps,resources=pods/finalizers,verbs=update
+//+kubebuilder:rbac:groups=apps,resources=deployments,verbs=get;list;watch;create;update;patch;delete
+//+kubebuilder:rbac:groups=apps,resources=deployments/status,verbs=get;update;patch
+//+kubebuilder:rbac:groups=apps,resources=deployments/finalizers,verbs=update
 
 // Reconcile is part of the main kubernetes reconciliation loop which aims to
 // move the current state of the cluster closer to the desired state.
 // TODO(user): Modify the Reconcile function to compare the state specified by
-// the Pod object against the actual cluster state, and then
+// the Deployment object against the actual cluster state, and then
 // perform operations to make the cluster state reflect the state specified by
 // the user.
 //
 // For more details, check Reconcile and its Result here:
 // - https://pkg.go.dev/sigs.k8s.io/controller-runtime@v0.7.0/pkg/reconcile
-func (r *PodReconciler) Reconcile(ctx context.Context, req ctrl.Request) (ctrl.Result, error) {
-	_ = r.Log.WithValues("pod", req.NamespacedName)
+func (r *DeploymentReconciler) Reconcile(ctx context.Context, req ctrl.Request) (ctrl.Result, error) {
+	_ = r.Log.WithValues("deployment", req.NamespacedName)
 
 	// your logic here
 
@@ -54,9 +55,8 @@ func (r *PodReconciler) Reconcile(ctx context.Context, req ctrl.Request) (ctrl.R
 }
 
 // SetupWithManager sets up the controller with the Manager.
-func (r *PodReconciler) SetupWithManager(mgr ctrl.Manager) error {
+func (r *DeploymentReconciler) SetupWithManager(mgr ctrl.Manager) error {
 	return ctrl.NewControllerManagedBy(mgr).
-		// Uncomment the following line adding a pointer to an instance of the controlled resource as an argument
-		// For().
+		For(&appsv1.Deployment{}).
 		Complete(r)
 }
diff --git a/testdata/project-v3-multigroup/controllers/apps/suite_test.go b/testdata/project-v3-multigroup/controllers/apps/suite_test.go
index 8dedd70d4ac..d0c244d0aed 100644
--- a/testdata/project-v3-multigroup/controllers/apps/suite_test.go
+++ b/testdata/project-v3-multigroup/controllers/apps/suite_test.go
@@ -22,6 +22,7 @@ import (
 
 	. "github.com/onsi/ginkgo"
 	. "github.com/onsi/gomega"
+	appsv1 "k8s.io/api/apps/v1"
 	"k8s.io/client-go/kubernetes/scheme"
 	"k8s.io/client-go/rest"
 	"sigs.k8s.io/controller-runtime/pkg/client"
@@ -60,6 +61,9 @@ var _ = BeforeSuite(func() {
 	Expect(err).NotTo(HaveOccurred())
 	Expect(cfg).NotTo(BeNil())
 
+	err = appsv1.AddToScheme(scheme.Scheme)
+	Expect(err).NotTo(HaveOccurred())
+
 	//+kubebuilder:scaffold:scheme
 
 	k8sClient, err = client.New(cfg, client.Options{Scheme: scheme.Scheme})
diff --git a/testdata/project-v3-multigroup/main.go b/testdata/project-v3-multigroup/main.go
index d79bb749908..5707341bd7f 100644
--- a/testdata/project-v3-multigroup/main.go
+++ b/testdata/project-v3-multigroup/main.go
@@ -169,12 +169,12 @@ func main() {
 		setupLog.Error(err, "unable to create controller", "controller", "HealthCheckPolicy")
 		os.Exit(1)
 	}
-	if err = (&appscontrollers.PodReconciler{
+	if err = (&appscontrollers.DeploymentReconciler{
 		Client: mgr.GetClient(),
-		Log:    ctrl.Log.WithName("controllers").WithName("apps").WithName("Pod"),
+		Log:    ctrl.Log.WithName("controllers").WithName("apps").WithName("Deployment"),
 		Scheme: mgr.GetScheme(),
 	}).SetupWithManager(mgr); err != nil {
-		setupLog.Error(err, "unable to create controller", "controller", "Pod")
+		setupLog.Error(err, "unable to create controller", "controller", "Deployment")
 		os.Exit(1)
 	}
 	if err = (&controllers.LakersReconciler{
diff --git a/testdata/project-v3/PROJECT b/testdata/project-v3/PROJECT
index b30361d9899..8dde5b76ffe 100644
--- a/testdata/project-v3/PROJECT
+++ b/testdata/project-v3/PROJECT
@@ -40,4 +40,9 @@ resources:
   webhooks:
     defaulting: true
     webhookVersion: v1
+- controller: true
+  domain: testproject.org
+  group: crew
+  kind: Laker
+  version: v1
 version: "3"