MySQL InnoDB not releasing disk space after deleting data rows from table

If you don't use innodb_file_per_table, reclaiming disk space is possible, but quite tedious, and requires a significant amount of downtime.

The How To is pretty in-depth - but I pasted the relevant part below.

Be sure to also retain a copy of your schema in your dump.

Currently, you cannot remove a data file from the system tablespace. To decrease the system tablespace size, use this procedure:

Use mysqldump to dump all your InnoDB tables.

Stop the server.

Remove all the existing tablespace files, including the ibdata and ib_log files. If you want to keep a backup copy of the information, then copy all the ib* files to another location before the removing the files in your MySQL installation.

Remove any .frm files for InnoDB tables.

Configure a new tablespace.

Restart the server.

Import the dump files.

MySQL doesn't reduce the size of ibdata1. Ever. Even if you use optimize table to free the space used from deleted records, it will reuse it later.

An alternative is to configure the server to use innodb_file_per_table, but this will require a backup, drop database and restore. The positive side is that the .ibd file for the table is reduced after an optimize table.

Just had the same problem myself.

What happens is, that even if you drop the database, innodb will still not release disk space. I had to export, stop mysql, remove the files manually, start mysql, create database and users, and then import. Thank god I only had 200MB worth of rows, but it spared 250GB of innodb file.

Fail by design.