Not every database belongs to a website.
WHAT ELSE USES DATABASES
Roundcube webmail, which stores contacts and preferences Some cPanel features Applications installed through Softaculous Scripts you or a developer added
IDENTIFYING THEM
cPanel > MySQL Databases lists everything. Some may not obviously correspond to a site.
Read the applications' configuration files to map them.
WHAT NOT TO DELETE
Anything you cannot positively identify. Deleting a database an application depends on breaks it, and the connection to the cause is not obvious weeks later.
DATABASES FROM REMOVED APPLICATIONS
These are safe to remove, and they do accumulate.
Before removing, export and keep the dump for a period in case something was overlooked.
SOFTACULOUS INSTALLATIONS
Removing an installation through Softaculous deletes its database and user together, which is tidier than doing it by hand.
Softaculous > Installations lists what it created.
THE AUDIT WORTH DOING
Once a year, list every database and identify what uses it. You will find things you had forgotten.
