diff --git a/.github/workflows/e2e.yaml b/.github/workflows/e2e.yaml
index bcf08f43..0c046f40 100644
--- a/.github/workflows/e2e.yaml
+++ b/.github/workflows/e2e.yaml
@@ -238,6 +238,9 @@ jobs:
       - name: flux check
         run: |
           ./bin/flux check
+      - name: flux migrate
+        run: |
+          ./bin/flux migrate
       - name: flux version
         run: |
           ./bin/flux version
diff --git a/cmd/flux/migrate.go b/cmd/flux/migrate.go
new file mode 100644
index 00000000..4c304a72
--- /dev/null
+++ b/cmd/flux/migrate.go
@@ -0,0 +1,184 @@
+/*
+Copyright 2025 The Flux 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 main
+
+import (
+	"context"
+	"fmt"
+
+	"github.com/spf13/cobra"
+	apiextensionsv1 "k8s.io/apiextensions-apiserver/pkg/apis/apiextensions/v1"
+	apierrors "k8s.io/apimachinery/pkg/api/errors"
+	"k8s.io/apimachinery/pkg/apis/meta/v1/unstructured"
+	"k8s.io/client-go/util/retry"
+	"sigs.k8s.io/controller-runtime/pkg/client"
+
+	"github.com/fluxcd/flux2/v2/internal/utils"
+)
+
+var migrateCmd = &cobra.Command{
+	Use:   "migrate",
+	Args:  cobra.NoArgs,
+	Short: "Migrate the Flux custom resources to their latest API version",
+	Long: `The migrate command must be run before a Flux minor version upgrade.
+The command migrates the Flux custom resources stored in Kubernetes etcd to their latest API version,
+ensuring the Flux components can continue to function correctly after the upgrade.
+`,
+	RunE: runMigrateCmd,
+}
+
+func init() {
+	rootCmd.AddCommand(migrateCmd)
+}
+
+func runMigrateCmd(cmd *cobra.Command, args []string) error {
+	logger.Actionf("starting migration of custom resources")
+	ctx, cancel := context.WithTimeout(context.Background(), rootArgs.timeout)
+	defer cancel()
+
+	cfg, err := utils.KubeConfig(kubeconfigArgs, kubeclientOptions)
+	if err != nil {
+		return fmt.Errorf("Kubernetes client initialization failed: %s", err.Error())
+	}
+
+	kubeClient, err := client.New(cfg, client.Options{Scheme: utils.NewScheme()})
+	if err != nil {
+		return err
+	}
+
+	migrator := NewMigrator(kubeClient, client.MatchingLabels{
+		"app.kubernetes.io/part-of": "flux",
+	})
+
+	if err := migrator.Run(ctx); err != nil {
+		return err
+	}
+
+	logger.Successf("custom resources migrated successfully")
+	return nil
+}
+
+type Migrator struct {
+	labelSelector client.MatchingLabels
+	kubeClient    client.Client
+}
+
+// NewMigrator creates a new Migrator instance with the specified label selector.
+func NewMigrator(kubeClient client.Client, labelSelector client.MatchingLabels) *Migrator {
+	return &Migrator{
+		labelSelector: labelSelector,
+		kubeClient:    kubeClient,
+	}
+}
+
+func (m *Migrator) Run(ctx context.Context) error {
+	crdList := &apiextensionsv1.CustomResourceDefinitionList{}
+
+	if err := m.kubeClient.List(ctx, crdList, m.labelSelector); err != nil {
+		return fmt.Errorf("failed to list CRDs: %w", err)
+	}
+
+	for _, crd := range crdList.Items {
+		if err := m.migrateCRD(ctx, crd.Name); err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+func (m *Migrator) migrateCRD(ctx context.Context, name string) error {
+	crd := &apiextensionsv1.CustomResourceDefinition{}
+
+	if err := m.kubeClient.Get(ctx, client.ObjectKey{Name: name}, crd); err != nil {
+		return fmt.Errorf("failed to get CRD %s: %w", name, err)
+	}
+
+	// get the latest storage version for the CRD
+	storageVersion := m.getStorageVersion(crd)
+	if storageVersion == "" {
+		return fmt.Errorf("no storage version found for CRD %s", name)
+	}
+
+	// migrate all the resources for the CRD
+	err := retry.RetryOnConflict(retry.DefaultRetry, func() error {
+		return m.migrateCR(ctx, crd, storageVersion)
+	})
+	if err != nil {
+		return fmt.Errorf("failed to migrate resources for CRD %s: %w", name, err)
+	}
+
+	// set the CRD status to contain only the latest storage version
+	if len(crd.Status.StoredVersions) > 1 || crd.Status.StoredVersions[0] != storageVersion {
+		crd.Status.StoredVersions = []string{storageVersion}
+		if err := m.kubeClient.Status().Update(ctx, crd); err != nil {
+			return fmt.Errorf("failed to update CRD %s status: %w", crd.Name, err)
+		}
+		logger.Successf("%s migrated to storage version %s", crd.Name, storageVersion)
+	}
+	return nil
+}
+
+// migrateCR migrates all CRs for the given CRD to the specified version by patching them with an empty patch.
+func (m *Migrator) migrateCR(ctx context.Context, crd *apiextensionsv1.CustomResourceDefinition, version string) error {
+	list := &unstructured.UnstructuredList{}
+
+	apiVersion := crd.Spec.Group + "/" + version
+	listKind := crd.Spec.Names.ListKind
+
+	list.SetAPIVersion(apiVersion)
+	list.SetKind(listKind)
+
+	err := m.kubeClient.List(ctx, list, client.InNamespace(""))
+	if err != nil {
+		return fmt.Errorf("failed to list resources for CRD %s: %w", crd.Name, err)
+	}
+
+	if len(list.Items) == 0 {
+		return nil
+	}
+
+	for _, item := range list.Items {
+		// patch the resource with an empty patch to update the version
+		if err := m.kubeClient.Patch(
+			ctx,
+			&item,
+			client.RawPatch(client.Merge.Type(), []byte("{}")),
+		); err != nil && !apierrors.IsNotFound(err) {
+			return fmt.Errorf(" %s/%s/%s failed to migrate: %w",
+				item.GetKind(), item.GetNamespace(), item.GetName(), err)
+		}
+
+		logger.Successf("%s/%s/%s migrated to version %s",
+			item.GetKind(), item.GetNamespace(), item.GetName(), version)
+	}
+
+	return nil
+}
+
+// getStorageVersion retrieves the storage version of a CustomResourceDefinition.
+func (m *Migrator) getStorageVersion(crd *apiextensionsv1.CustomResourceDefinition) string {
+	var version string
+	for _, v := range crd.Spec.Versions {
+		if v.Storage {
+			version = v.Name
+			break
+		}
+	}
+
+	return version
+}