diff --git a/pkg/rescaffold/migrate.go b/pkg/rescaffold/migrate.go
index 91854c24783..999ea78f929 100644
--- a/pkg/rescaffold/migrate.go
+++ b/pkg/rescaffold/migrate.go
@@ -100,8 +100,24 @@ func getOutputPath(currentWorkingDirectory, outputPath string) (string, error) {
 	return "", err
 }
 
-func kubebuilderInit(_ store.Store) error {
+func kubebuilderInit(store store.Store) error {
 	var args []string
 	args = append(args, "init")
+	args = append(args, getInitArgs(store)...)
 	return util.RunCmd("kubebuilder init", "kubebuilder", args...)
 }
+
+func getInitArgs(store store.Store) []string {
+	var args []string
+	plugins := store.Config().GetPluginChain()
+	if len(plugins) > 0 {
+		args = append(args, "--plugins")
+		args = append(args, plugins...)
+	}
+	domain := store.Config().GetDomain()
+	if domain != "" {
+		args = append(args, "--domain")
+		args = append(args, domain)
+	}
+	return args
+}
diff --git a/test/e2e/alphagenerate/e2e_suite_test.go b/test/e2e/alphagenerate/e2e_suite_test.go
new file mode 100644
index 00000000000..eab37e6dac4
--- /dev/null
+++ b/test/e2e/alphagenerate/e2e_suite_test.go
@@ -0,0 +1,32 @@
+/*
+Copyright 2023 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 alphagenerate
+
+import (
+	"fmt"
+	"testing"
+
+	. "github.com/onsi/ginkgo/v2"
+	. "github.com/onsi/gomega"
+)
+
+// Run e2e tests using the Ginkgo runner.
+func TestE2E(t *testing.T) {
+	RegisterFailHandler(Fail)
+	fmt.Fprintf(GinkgoWriter, "Starting kubebuilder suite test for the alpha command generate\n")
+	RunSpecs(t, "Kubebuilder alpha generate suite")
+}
diff --git a/test/e2e/alphagenerate/generate_test.go b/test/e2e/alphagenerate/generate_test.go
new file mode 100644
index 00000000000..b2d455a5131
--- /dev/null
+++ b/test/e2e/alphagenerate/generate_test.go
@@ -0,0 +1,96 @@
+/*
+Copyright 2023 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 alphagenerate
+
+import (
+	"fmt"
+	"path/filepath"
+
+	pluginutil "sigs.k8s.io/kubebuilder/v3/pkg/plugin/util"
+
+	. "github.com/onsi/ginkgo/v2"
+	. "github.com/onsi/gomega"
+
+	"sigs.k8s.io/kubebuilder/v3/test/e2e/utils"
+)
+
+var _ = Describe("kubebuilder", func() {
+	Context("alpha generate ", func() {
+		var (
+			kbc *utils.TestContext
+		)
+
+		BeforeEach(func() {
+			var err error
+			kbc, err = utils.NewTestContext(pluginutil.KubebuilderBinName, "GO111MODULE=on")
+			Expect(err).NotTo(HaveOccurred())
+			Expect(kbc.Prepare()).To(Succeed())
+		})
+
+		AfterEach(func() {
+			kbc.Destroy()
+		})
+
+		It("should regenerate the project with success", func() {
+			ReGenerateProject(kbc)
+		})
+
+	})
+})
+
+// ReGenerateProject implements a project that is regenerated by kubebuilder.
+func ReGenerateProject(kbc *utils.TestContext) {
+	var err error
+
+	By("initializing a project")
+	err = kbc.Init(
+		"--plugins", "go/v4",
+		"--project-version", "3",
+		"--domain", kbc.Domain,
+	)
+	ExpectWithOffset(1, err).NotTo(HaveOccurred())
+
+	By("regenerating the project")
+	err = kbc.Regenerate(
+		"--input-dir", kbc.Dir,
+		"--output-dir", filepath.Join(kbc.Dir, "testdir"),
+	)
+	ExpectWithOffset(1, err).NotTo(HaveOccurred())
+
+	By("checking if the project file was generated with the expected layout")
+	var layout = `layout:
+- go.kubebuilder.io/v4
+`
+	fileContainsExpr, err := pluginutil.HasFileContentWith(
+		filepath.Join(kbc.Dir, "testdir", "PROJECT"), layout)
+	ExpectWithOffset(1, err).NotTo(HaveOccurred())
+	ExpectWithOffset(1, fileContainsExpr).To(BeTrue())
+
+	By("checking if the project file was generated with the expected domain")
+	var domain = fmt.Sprintf("domain: %s", kbc.Domain)
+	fileContainsExpr, err = pluginutil.HasFileContentWith(
+		filepath.Join(kbc.Dir, "testdir", "PROJECT"), domain)
+	ExpectWithOffset(1, err).NotTo(HaveOccurred())
+	ExpectWithOffset(1, fileContainsExpr).To(BeTrue())
+
+	By("checking if the project file was generated with the expected version")
+	var version = `version: "3"`
+	fileContainsExpr, err = pluginutil.HasFileContentWith(
+		filepath.Join(kbc.Dir, "testdir", "PROJECT"), version)
+	ExpectWithOffset(1, err).NotTo(HaveOccurred())
+	ExpectWithOffset(1, fileContainsExpr).To(BeTrue())
+}
diff --git a/test/e2e/setup.sh b/test/e2e/setup.sh
index 20e7a9852fa..15210adafc3 100755
--- a/test/e2e/setup.sh
+++ b/test/e2e/setup.sh
@@ -66,6 +66,7 @@ function test_cluster {
   go test $(dirname "$0")/deployimage $flags -timeout 30m
   go test $(dirname "$0")/v4 $flags -timeout 30m
   go test $(dirname "$0")/externalplugin $flags -timeout 30m
+  go test $(dirname "$0")/alphagenerate $flags -timeout 30m
 }
 
 function build_sample_external_plugin {
diff --git a/test/e2e/utils/test_context.go b/test/e2e/utils/test_context.go
index d9630d6c7d8..6a0f61deedb 100644
--- a/test/e2e/utils/test_context.go
+++ b/test/e2e/utils/test_context.go
@@ -214,6 +214,15 @@ func (t *TestContext) CreateWebhook(resourceOptions ...string) error {
 	return err
 }
 
+// Regenerate is for running `kubebuilder alpha generate`
+func (t *TestContext) Regenerate(resourceOptions ...string) error {
+	resourceOptions = append([]string{"alpha", "generate"}, resourceOptions...)
+	//nolint:gosec
+	cmd := exec.Command(t.BinaryName, resourceOptions...)
+	_, err := t.Run(cmd)
+	return err
+}
+
 // Make is for running `make` with various targets
 func (t *TestContext) Make(makeOptions ...string) error {
 	cmd := exec.Command("make", makeOptions...)