Server Maintenance | Updated 2026
Regularly repairing and optimizing MySQL/MariaDB tables reclaims unused space, fixes corrupted indexes, and improves query performance. Here is how to do it at both the account and server level.
Account Level (cPanel)
Optimize via phpMyAdmin
phpMyAdmin > select your database > check all tables > dropdown: "Optimize table." Or use SSH: mysqlcheck -u dbuser -p --optimize dbname
01. Server-Wide Optimization (Root)
# Check, repair, and optimize all databases
mysqlcheck -u root -p --all-databases --check --optimize --auto-repair
# Or separately:
mysqlcheck -u root -p --all-databases --repair
mysqlcheck -u root -p --all-databases --optimize02. Automate With Cron
# Weekly optimization - add to root crontab
0 3 * * 0 mysqlcheck -u root --all-databases --optimize --auto-repair >/dev/null 2>&1InnoDB Note
For InnoDB tables, OPTIMIZE TABLE actually performs a table rebuild (ALTER TABLE ... ENGINE=InnoDB). This can temporarily lock the table and use significant disk space for large tables. Run during low-traffic periods. For ibdata1 bloat, see Shrink ibdata1.
For backups before maintenance: Backup MySQL.
Database Issues?
Open a Support TicketQuick Recap
- phpMyAdmin: Check all > Optimize table
- SSH:
mysqlcheck --optimize --auto-repair - Server-wide:
--all-databasesflag (root only) - Automate weekly via cron
- InnoDB optimize rebuilds tables - Run off-peak
Database maintenance · Last updated March 2026 · Browse all Server Maintenance articles
