You could have InnoDB clean things up as follows: - signal mysqld to have InnoDB flush everything out of the logs on shutdown - shutdown mysqld - delete the logs - start mysqld No crash recovery will happen because there will be nothing to recover. MYSQL_USER=root MYSQL_PASS=rootpassword MYSQL_CONN="-u${MYSQL_CONN} -p${MYSQL_PASS} -h127.0.0.1 -P3306 --protocol=tcp" SQL="SET GLOBAL innodb_fast_shutdown = 0" mysql ${MYSQL_CONN} -ANe"${SQL}" mysqladmin ${MYSQL_CONN} shutdown cd /var/lib/mysql rm -f ib_logfile* service mysql start If you want lingering data pages cleansed out of the Double Write Buffer, please see my old post http://dba.stackexchange.com/questions/30611/fill-ibdata1-with-zeros-nulls-etc-or-change-a-tables-tablespace/30620#30620 #GIVE IT A TRY !!!