Disk quota for MySQL databases will show 0.00MB usage in under “MySQL Databases” in cPanel unless this option is selected in Tweak Settings in WHM (root.)

When displaying disk usage in cPanel/WHM include Postgresql and MySQL® disk usage. [Requires MySQL® 5+] (SQL disk usage is only updated every four hours)

Once you enable this settings under “Tweak Settings,” you will then need to log into SSH to run the following command that will update MySQL database’s disk space usage/quotas.

/scripts/update_db_cache