diff --git a/bootstrap.go b/bootstrap.go
index 06cdcc0036..0805b2b6d9 100644
--- a/bootstrap.go
+++ b/bootstrap.go
@@ -148,6 +148,7 @@ func checkBootstrappedVar(s Session) (bool, error) {
 		}
 		return false, errors.Trace(err)
 	}
+
 	if len(rs) != 1 {
 		return false, errors.New("Wrong number of Recordset")
 	}
@@ -156,7 +157,17 @@ func checkBootstrappedVar(s Session) (bool, error) {
 	if err != nil || row == nil {
 		return false, errors.Trace(err)
 	}
-	return row.Data[0].(string) == bootstrappedVarTrue, nil
+
+	isBootstrapped := row.Data[0].(string) == bootstrappedVarTrue
+	if isBootstrapped {
+		// Make sure that doesn't affect the following operations.
+
+		if err = s.FinishTxn(false); err != nil {
+			return false, errors.Trace(err)
+		}
+	}
+
+	return isBootstrapped, nil
 }
 
 // Execute DDL statements in bootstrap stage.
diff --git a/session_test.go b/session_test.go
index aacdcb9609..1c2a5dc3b7 100644
--- a/session_test.go
+++ b/session_test.go
@@ -719,6 +719,7 @@ func (s *testSessionSuite) TestBootstrap(c *C) {
 	se := newSession(c, store, s.dbName)
 	mustExecSQL(c, se, "USE mysql;")
 	r := mustExecSQL(c, se, `select * from user;`)
+	c.Assert(r, NotNil)
 	row, err := r.Next()
 	c.Assert(err, IsNil)
 	c.Assert(row, NotNil)
@@ -734,9 +735,31 @@ func (s *testSessionSuite) TestBootstrap(c *C) {
 	mustExecSQL(c, se, "SELECT * from mysql.columns_priv;")
 	// Check privilege tables.
 	r = mustExecSQL(c, se, "SELECT COUNT(*) from mysql.global_variables;")
+	c.Assert(r, NotNil)
 	v, err := r.FirstRow()
 	c.Assert(err, IsNil)
 	c.Assert(v[0], Equals, int64(len(variable.SysVars)))
+
+	// Check a storage operations are default autocommit after the second start.
+	mustExecSQL(c, se, "USE test;")
+	mustExecSQL(c, se, "drop table if exists t")
+	mustExecSQL(c, se, "create table t (id int)")
+	delete(storeBootstrapped, store.UUID())
+	se.Close()
+	se, err = CreateSession(store)
+	c.Assert(err, IsNil)
+	mustExecSQL(c, se, "USE test;")
+	mustExecSQL(c, se, "insert t values (?)", 3)
+	se, err = CreateSession(store)
+	c.Assert(err, IsNil)
+	mustExecSQL(c, se, "USE test;")
+	r = mustExecSQL(c, se, "select * from t")
+	c.Assert(r, NotNil)
+	v, err = r.FirstRow()
+	c.Assert(err, IsNil)
+	match(c, v, 3)
+	mustExecSQL(c, se, "drop table if exists t")
+	se.Close()
 }
 
 // Create a new session on store but only do ddl works.