diff --git a/pkg/agent/controller/endpoint_slice.go b/pkg/agent/controller/endpoint_slice.go
index 67cb1ba0e..afd0a9125 100644
--- a/pkg/agent/controller/endpoint_slice.go
+++ b/pkg/agent/controller/endpoint_slice.go
@@ -99,16 +99,14 @@ func (c *EndpointSliceController) start(stopCh <-chan struct{}) error {
 
 func (c *EndpointSliceController) onLocalEndpointSlice(obj runtime.Object, _ int, op syncer.Operation) (runtime.Object, bool) {
 	endpointSlice := obj.(*discovery.EndpointSlice)
-	labels := endpointSlice.GetObjectMeta().GetLabels()
 
-	oldName := labels[mcsv1a1.LabelServiceName] + "-" + labels[constants.MCSLabelSourceCluster]
-	if op != syncer.Delete && endpointSlice.Name == oldName {
-		logger.Infof("EndpointSlice %s/%s has the old naming convention sans namespace - deleting it",
+	if op != syncer.Delete && isLegacyEndpointSlice(endpointSlice) {
+		logger.Infof("Found legacy EndpointSlice %s/%s - deleting it",
 			endpointSlice.Namespace, endpointSlice.Name)
 
 		err := c.syncer.GetLocalFederator().Delete(endpointSlice)
 		if err != nil {
-			logger.Errorf(err, "Error deleting local EndpointSlice %s/%s", endpointSlice.Namespace, endpointSlice.Name)
+			logger.Errorf(err, "Error deleting legacy EndpointSlice %s/%s", endpointSlice.Namespace, endpointSlice.Name)
 		}
 
 		return nil, false
@@ -117,6 +115,22 @@ func (c *EndpointSliceController) onLocalEndpointSlice(obj runtime.Object, _ int
 	return obj, false
 }
 
+func isLegacyEndpointSlice(endpointSlice *discovery.EndpointSlice) bool {
+	// The original name sans namespace prior to 0.15.
+	origName := endpointSlice.Labels[mcsv1a1.LabelServiceName] + "-" + endpointSlice.Labels[constants.MCSLabelSourceCluster]
+	if endpointSlice.Name == origName {
+		return true
+	}
+
+	// Check for headless EndpointSlice derived from service Endpoints prior to 0.16.
+	if endpointSlice.Labels[constants.LabelIsHeadless] == strconv.FormatBool(true) &&
+		strings.HasPrefix(endpointSlice.Name, endpointSlice.Labels[mcsv1a1.LabelServiceName]+"-"+endpointSlice.Namespace) {
+		return true
+	}
+
+	return false
+}
+
 func (c *EndpointSliceController) onRemoteEndpointSlice(obj runtime.Object, _ int, _ syncer.Operation) (runtime.Object, bool) {
 	endpointSlice := obj.(*discovery.EndpointSlice)
 	endpointSlice.Namespace = endpointSlice.GetObjectMeta().GetLabels()[constants.LabelSourceNamespace]
diff --git a/pkg/agent/controller/reconciliation_test.go b/pkg/agent/controller/reconciliation_test.go
index 9842ec835..03ba5cdff 100644
--- a/pkg/agent/controller/reconciliation_test.go
+++ b/pkg/agent/controller/reconciliation_test.go
@@ -20,6 +20,8 @@ package controller_test
 
 import (
 	"context"
+	"fmt"
+	"strconv"
 	"strings"
 
 	. "github.com/onsi/ginkgo/v2"
@@ -229,6 +231,22 @@ var _ = Describe("Reconciliation", func() {
 				t.cluster1.service.Name, t.cluster1.clusterID)
 		})
 	})
+})
+
+var _ = Describe("EndpointSlice migration", func() {
+	var t *testDriver
+
+	BeforeEach(func() {
+		t = newTestDiver()
+	})
+
+	JustBeforeEach(func() {
+		t.justBeforeEach()
+	})
+
+	AfterEach(func() {
+		t.afterEach()
+	})
 
 	When("a local EndpointSlice with the old naming convention sans namespace exists on startup", func() {
 		epsName := "nginx-" + clusterID1
@@ -257,4 +275,33 @@ var _ = Describe("Reconciliation", func() {
 			test.AwaitNoResource(t.brokerEndpointSliceClient, epsName)
 		})
 	})
+
+	When("a legacy local EndpointSlice derived from Endpoints exists on startup", func() {
+		epsName := fmt.Sprintf("nginx-%s-%s", serviceNamespace, clusterID1)
+
+		JustBeforeEach(func() {
+			eps := &discovery.EndpointSlice{
+				ObjectMeta: metav1.ObjectMeta{
+					Name:      epsName,
+					Namespace: serviceNamespace,
+					Labels: map[string]string{
+						discovery.LabelManagedBy:        constants.LabelValueManagedBy,
+						constants.MCSLabelSourceCluster: clusterID1,
+						mcsv1a1.LabelServiceName:        "nginx",
+						constants.LabelIsHeadless:       strconv.FormatBool(true),
+					},
+				},
+			}
+
+			test.CreateResource(t.cluster1.localEndpointSliceClient, eps)
+
+			eps.Namespace = test.RemoteNamespace
+			test.CreateResource(t.brokerEndpointSliceClient, test.SetClusterIDLabel(eps, clusterID1))
+		})
+
+		It("should delete it", func() {
+			test.AwaitNoResource(t.cluster1.localEndpointSliceClient, epsName)
+			test.AwaitNoResource(t.brokerEndpointSliceClient, epsName)
+		})
+	})
 })