diff --git a/go/mysql/conn.go b/go/mysql/conn.go
index c7492aec35c..2400834a75b 100644
--- a/go/mysql/conn.go
+++ b/go/mysql/conn.go
@@ -199,6 +199,12 @@ type Conn struct {
 	// enableQueryInfo controls whether we parse the INFO field in QUERY_OK packets
 	// See: ConnParams.EnableQueryInfo
 	enableQueryInfo bool
+
+	// mu protects the fields below
+	mu sync.Mutex
+	// this is used to mark the connection to be closed so that the command phase for the connection can be stopped and
+	// the connection gets closed.
+	closing bool
 }
 
 // splitStatementFunciton is the function that is used to split the statement in case of a multi-statement query.
@@ -895,6 +901,11 @@ func (c *Conn) handleNextCommand(handler Handler) bool {
 		return false
 	}
 
+	// before continue to process the packet, check if the connection should be closed or not.
+	if c.IsMarkedForClose() {
+		return false
+	}
+
 	switch data[0] {
 	case ComQuit:
 		c.recycleReadPacket()
@@ -1581,3 +1592,21 @@ func (c *Conn) IsUnixSocket() bool {
 func (c *Conn) GetRawConn() net.Conn {
 	return c.conn
 }
+
+// MarkForClose marks the connection for close.
+func (c *Conn) MarkForClose() {
+	c.mu.Lock()
+	defer c.mu.Unlock()
+	c.closing = true
+}
+
+// IsMarkedForClose return true if the connection should be closed.
+func (c *Conn) IsMarkedForClose() bool {
+	c.mu.Lock()
+	defer c.mu.Unlock()
+	return c.closing
+}
+
+func (c *Conn) IsShuttingDown() bool {
+	return c.listener.isShutdown()
+}
diff --git a/go/mysql/server.go b/go/mysql/server.go
index c32f0d6d85f..68ac11e1adf 100644
--- a/go/mysql/server.go
+++ b/go/mysql/server.go
@@ -520,7 +520,8 @@ func (l *Listener) handle(conn net.Conn, connectionID uint32, acceptTime time.Ti
 
 	for {
 		kontinue := c.handleNextCommand(l.handler)
-		if !kontinue {
+		// before going for next command check if the connection should be closed or not.
+		if !kontinue || c.IsMarkedForClose() {
 			return
 		}
 	}
diff --git a/go/vt/vtgate/plugin_mysql_server.go b/go/vt/vtgate/plugin_mysql_server.go
index f880b6c0412..e0ed4c94d97 100644
--- a/go/vt/vtgate/plugin_mysql_server.go
+++ b/go/vt/vtgate/plugin_mysql_server.go
@@ -182,6 +182,12 @@ func startSpan(ctx context.Context, query, label string) (trace.Span, context.Co
 }
 
 func (vh *vtgateHandler) ComQuery(c *mysql.Conn, query string, callback func(*sqltypes.Result) error) error {
+	session := vh.session(c)
+	if c.IsShuttingDown() && !session.InTransaction {
+		c.MarkForClose()
+		return mysql.NewSQLError(mysql.ERServerShutdown, mysql.SSNetError, "Server shutdown in progress")
+	}
+
 	ctx := context.Background()
 	var cancel context.CancelFunc
 	if *mysqlQueryTimeout != 0 {
@@ -209,7 +215,6 @@ func (vh *vtgateHandler) ComQuery(c *mysql.Conn, query string, callback func(*sq
 		"VTGate MySQL Connector" /* subcomponent: part of the client */)
 	ctx = callerid.NewContext(ctx, ef, im)
 
-	session := vh.session(c)
 	if !session.InTransaction {
 		atomic.AddInt32(&busyConnections, 1)
 	}
@@ -536,11 +541,11 @@ func newMysqlUnixSocket(address string, authServer mysql.AuthServer, handler mys
 
 func shutdownMysqlProtocolAndDrain() {
 	if mysqlListener != nil {
-		mysqlListener.Close()
+		mysqlListener.Shutdown()
 		mysqlListener = nil
 	}
 	if mysqlUnixListener != nil {
-		mysqlUnixListener.Close()
+		mysqlUnixListener.Shutdown()
 		mysqlUnixListener = nil
 	}
 	if sigChan != nil {