diff --git a/server/etcdserver/server.go b/server/etcdserver/server.go
index ac5f0c7ab293..ddb6e83e39a7 100644
--- a/server/etcdserver/server.go
+++ b/server/etcdserver/server.go
@@ -1809,6 +1809,11 @@ func (s *EtcdServer) apply(
 			var cc raftpb.ConfChange
 			pbutil.MustUnmarshal(&cc, e.Data)
 			removedSelf, err := s.applyConfChange(cc, confState, shouldApplyV3)
+			if err != nil {
+				s.lg.Error("failed to apply conf change", zap.Bool("shouldApplyV3", bool(shouldApplyV3)), zap.Error(err))
+			} else {
+				s.KV().Commit()
+			}
 			s.setAppliedIndex(e.Index)
 			s.setTerm(e.Term)
 			shouldStop = shouldStop || removedSelf
diff --git a/server/etcdserver/server_test.go b/server/etcdserver/server_test.go
index 4b8a12f010e4..268496e1a049 100644
--- a/server/etcdserver/server_test.go
+++ b/server/etcdserver/server_test.go
@@ -298,6 +298,7 @@ func newServer(t *testing.T, recorder *nodeRecorder) *EtcdServer {
 		r:            *newRaftNode(raftNodeConfig{lg: lg, Node: recorder}),
 		cluster:      membership.NewCluster(lg),
 		consistIndex: cindex.NewConsistentIndex(be),
+		kv:           mvcc.New(zap.NewNop(), be, &lease.FakeLessor{}, mvcc.StoreConfig{}),
 	}
 	srv.cluster.SetBackend(schema.NewMembershipBackend(lg, be))
 	srv.cluster.SetStore(v2store.New())
diff --git a/tests/e2e/ctl_v3_member_no_proxy_test.go b/tests/e2e/ctl_v3_member_no_proxy_test.go
index 619ae5d136c1..e6d263b0c222 100644
--- a/tests/e2e/ctl_v3_member_no_proxy_test.go
+++ b/tests/e2e/ctl_v3_member_no_proxy_test.go
@@ -40,18 +40,17 @@ func TestMemberReplace(t *testing.T) {
 	require.NoError(t, err)
 	defer epc.Close()
 
-	memberId := rand.Int() % len(epc.Procs)
-	member := epc.Procs[memberId]
+	memberIdx := rand.Int() % len(epc.Procs)
+	member := epc.Procs[memberIdx]
 	memberName := member.Config().Name
 	var endpoints []string
 	for i := 1; i < len(epc.Procs); i++ {
-		endpoints = append(endpoints, epc.Procs[(memberId+i)%len(epc.Procs)].EndpointsGRPC()...)
+		endpoints = append(endpoints, epc.Procs[(memberIdx+i)%len(epc.Procs)].EndpointsGRPC()...)
 	}
 	cc, err := e2e.NewEtcdctl(epc.Cfg.Client, endpoints)
 	require.NoError(t, err)
 
-	c := epc.Etcdctl()
-	memberID, found, err := getMemberIdByName(ctx, c, memberName)
+	memberID, found, err := getMemberIdByName(ctx, cc, memberName)
 	require.NoError(t, err)
 	require.Equal(t, found, true, "Member not found")
 
@@ -59,9 +58,9 @@ func TestMemberReplace(t *testing.T) {
 	time.Sleep(etcdserver.HealthInterval)
 
 	t.Logf("Removing member %s", memberName)
-	_, err = c.MemberRemove(ctx, memberID)
+	_, err = cc.MemberRemove(ctx, memberID)
 	require.NoError(t, err)
-	_, found, err = getMemberIdByName(ctx, c, memberName)
+	_, found, err = getMemberIdByName(ctx, cc, memberName)
 	require.NoError(t, err)
 	require.Equal(t, found, false, "Expected member to be removed")
 	for member.IsRunning() {
@@ -82,12 +81,14 @@ func TestMemberReplace(t *testing.T) {
 	err = patchArgs(member.Config().Args, "initial-cluster-state", "existing")
 	require.NoError(t, err)
 
+	// Sleep 100ms to bypass the known issue https://github.com/etcd-io/etcd/issues/16687.
+	time.Sleep(100 * time.Millisecond)
 	t.Logf("Starting member %s", memberName)
 	err = member.Start(ctx)
 	require.NoError(t, err)
 	testutils.ExecuteUntil(ctx, t, func() {
 		for {
-			_, found, err := getMemberIdByName(ctx, c, memberName)
+			_, found, err := getMemberIdByName(ctx, cc, memberName)
 			if err != nil || !found {
 				time.Sleep(10 * time.Millisecond)
 				continue