Using System Variables does not change variable values, it has no effect on the contents of the  variables_info  table until the server is restarted. The  mysqld-auto.cnf  file uses a  JSON  format like this (reformatted slightly for readability): At startup, the server processes the  mysqld-auto.cnf  file after all other option files (see Section 4.2.2.2, “Using Option Files” ). The server handles the file contents as follows: Format and Server Handling of the mysqld-auto.cnf File { "Version": 1, "mysql_server": { "max_connections": { "Value": "152", "Metadata": { "Timestamp": 1519921341372531, "User": "root", "Host": "localhost" } }, "transaction_isolation": { "Value": "READ-COMMITTED", "Metadata": { "Timestamp": 1519921553880520, "User": "root", "Host": "localhost" } }, "mysql_server_static_options": { "innodb_api_enable_mdl": { "Value": "0", "Metadata": { "Timestamp": 1519922873467872, "User": "root", "Host": "localhost" } }, "log_slave_updates": { "Value": "1", "Metadata": { "Timestamp": 1519925628441588, "User": "root", "Host": "localhost" } } } } } •If the  persisted_globals_load  system variable is disabled, the server ignores the  mysqld- auto.cnf  file. •The  "mysql_server_static_options"  section contains read-only variables persisted using  SET PERSIST_ONLY . The section may also (despite its name) contain certain dynamic variables that are not read only. All variables present inside this section are appended to the command line and processed with other command-line options. •All remaining persisted variables are set by executing the equivalent of a  SET GLOBAL  statement later, just before the server starts listening for client connections. These settings therefore do not take effect until late in the startup process, which might be unsuitable for certain system variables. It may be preferable to set such variables in  my.cnf  rather than in  mysqld-auto.cnf . 941