diff --git a/etcdserver/apply.go b/etcdserver/apply.go
index 822b5e322..22e0e8543 100644
--- a/etcdserver/apply.go
+++ b/etcdserver/apply.go
@@ -21,7 +21,10 @@ import (
 	"sort"
 	"time"
 
+	"github.com/coreos/go-semver/semver"
 	"go.etcd.io/etcd/auth"
+	"go.etcd.io/etcd/etcdserver/api"
+	"go.etcd.io/etcd/etcdserver/api/membership/membershippb"
 	pb "go.etcd.io/etcd/etcdserver/etcdserverpb"
 	"go.etcd.io/etcd/lease"
 	"go.etcd.io/etcd/mvcc"
@@ -47,6 +50,11 @@ type applyResult struct {
 	trace *traceutil.Trace
 }
 
+// applierV3Internal is the interface for processing internal V3 raft request
+type applierV3Internal interface {
+	ClusterVersionSet(r *membershippb.ClusterVersionSetRequest)
+}
+
 // applierV3 is the interface for processing V3 raft messages
 type applierV3 interface {
 	Apply(r *pb.InternalRaftRequest) *applyResult
@@ -104,6 +112,11 @@ func (s *EtcdServer) newApplierV3Backend() applierV3 {
 	return base
 }
 
+func (s *EtcdServer) newApplierV3Internal() applierV3Internal {
+	base := &applierV3backend{s: s}
+	return base
+}
+
 func (s *EtcdServer) newApplierV3() applierV3 {
 	return newAuthApplierV3(
 		s.AuthStore(),
@@ -170,6 +183,8 @@ func (a *applierV3backend) Apply(r *pb.InternalRaftRequest) *applyResult {
 		ar.resp, ar.err = a.s.applyV3.UserList(r.AuthUserList)
 	case r.AuthRoleList != nil:
 		ar.resp, ar.err = a.s.applyV3.RoleList(r.AuthRoleList)
+	case r.ClusterVersionSet != nil:
+		a.s.applyV3Internal.ClusterVersionSet(r.ClusterVersionSet)
 	default:
 		panic("not implemented")
 	}
@@ -833,6 +848,10 @@ func (a *applierV3backend) RoleList(r *pb.AuthRoleListRequest) (*pb.AuthRoleList
 	return resp, err
 }
 
+func (a *applierV3backend) ClusterVersionSet(r *membershippb.ClusterVersionSetRequest) {
+	a.s.cluster.SetVersion(semver.Must(semver.NewVersion(r.Ver)), api.UpdateCapability)
+}
+
 type quotaApplierV3 struct {
 	applierV3
 	q Quota
diff --git a/etcdserver/server.go b/etcdserver/server.go
index 4db1998d6..dbcf058ee 100644
--- a/etcdserver/server.go
+++ b/etcdserver/server.go
@@ -32,6 +32,7 @@ import (
 	"go.etcd.io/etcd/auth"
 	"go.etcd.io/etcd/etcdserver/api"
 	"go.etcd.io/etcd/etcdserver/api/membership"
+	"go.etcd.io/etcd/etcdserver/api/membership/membershippb"
 	"go.etcd.io/etcd/etcdserver/api/rafthttp"
 	"go.etcd.io/etcd/etcdserver/api/snap"
 	"go.etcd.io/etcd/etcdserver/api/v2discovery"
@@ -239,7 +240,9 @@ type EtcdServer struct {
 	applyV3 applierV3
 	// applyV3Base is the core applier without auth or quotas
 	applyV3Base applierV3
-	applyWait   wait.WaitTime
+	// applyV3Internal is the applier for internal request
+	applyV3Internal applierV3Internal
+	applyWait       wait.WaitTime
 
 	kv         mvcc.ConsistentWatchableKV
 	lessor     lease.Lessor
@@ -592,6 +595,7 @@ func NewServer(cfg ServerConfig) (srv *EtcdServer, err error) {
 	}
 
 	srv.applyV3Base = srv.newApplierV3Backend()
+	srv.applyV3Internal = srv.newApplierV3Internal()
 	if err = srv.restoreAlarms(); err != nil {
 		return nil, err
 	}
@@ -2527,14 +2531,10 @@ func (s *EtcdServer) updateClusterVersion(ver string) {
 		}
 	}
 
-	req := pb.Request{
-		Method: "PUT",
-		Path:   membership.StoreClusterVersionKey(),
-		Val:    ver,
-	}
+	req := membershippb.ClusterVersionSetRequest{Ver: ver}
 
 	ctx, cancel := context.WithTimeout(s.ctx, s.Cfg.ReqTimeout())
-	_, err := s.Do(ctx, req)
+	_, err := s.raftRequest(ctx, pb.InternalRaftRequest{ClusterVersionSet: &req})
 	cancel()
 
 	switch err {
diff --git a/etcdserver/server_test.go b/etcdserver/server_test.go
index c64471022..4c5d5883f 100644
--- a/etcdserver/server_test.go
+++ b/etcdserver/server_test.go
@@ -21,7 +21,6 @@ import (
 	"io/ioutil"
 	"net/http"
 	"os"
-	"path"
 	"path/filepath"
 	"reflect"
 	"sync"
@@ -1505,53 +1504,6 @@ func TestPublishRetry(t *testing.T) {
 	<-ch
 }
 
-func TestUpdateVersion(t *testing.T) {
-	n := newNodeRecorder()
-	ch := make(chan interface{}, 1)
-	// simulate that request has gone through consensus
-	ch <- Response{}
-	w := wait.NewWithResponse(ch)
-	ctx, cancel := context.WithCancel(context.TODO())
-	srv := &EtcdServer{
-		lgMu:       new(sync.RWMutex),
-		lg:         zap.NewExample(),
-		id:         1,
-		Cfg:        ServerConfig{Logger: zap.NewExample(), TickMs: 1, SnapshotCatchUpEntries: DefaultSnapshotCatchUpEntries},
-		r:          *newRaftNode(raftNodeConfig{lg: zap.NewExample(), Node: n}),
-		attributes: membership.Attributes{Name: "node1", ClientURLs: []string{"http://node1.com"}},
-		cluster:    &membership.RaftCluster{},
-		w:          w,
-		reqIDGen:   idutil.NewGenerator(0, time.Time{}),
-		SyncTicker: &time.Ticker{},
-
-		ctx:    ctx,
-		cancel: cancel,
-	}
-	srv.updateClusterVersion("2.0.0")
-
-	action := n.Action()
-	if len(action) != 1 {
-		t.Fatalf("len(action) = %d, want 1", len(action))
-	}
-	if action[0].Name != "Propose" {
-		t.Fatalf("action = %s, want Propose", action[0].Name)
-	}
-	data := action[0].Params[0].([]byte)
-	var r pb.Request
-	if err := r.Unmarshal(data); err != nil {
-		t.Fatalf("unmarshal request error: %v", err)
-	}
-	if r.Method != "PUT" {
-		t.Errorf("method = %s, want PUT", r.Method)
-	}
-	if wpath := path.Join(StoreClusterPrefix, "version"); r.Path != wpath {
-		t.Errorf("path = %s, want %s", r.Path, wpath)
-	}
-	if r.Val != "2.0.0" {
-		t.Errorf("val = %s, want %s", r.Val, "2.0.0")
-	}
-}
-
 func TestStopNotify(t *testing.T) {
 	s := &EtcdServer{
 		lgMu: new(sync.RWMutex),