diff --git a/pkg/plugins/golang/options.go b/pkg/plugins/golang/options.go
index a6cb1a01f5c..892217da7ca 100644
--- a/pkg/plugins/golang/options.go
+++ b/pkg/plugins/golang/options.go
@@ -178,7 +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/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 55fba1b8e6b..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"
 )
 
@@ -178,7 +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/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/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/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-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/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"