In order to change the Database ENGINE from InnoDB to MyISAM you may follow these instructions.

Take the backup of the Database

mysqldump cpaneluser_databasename > cpaneluser_databasename.sql

Once you secure the Database you may create a file called DBlist.txt at path /home/cPanel_UserName, with the names of those databases on which you wish to execute the conversion script.

touch /home/cPanel_UserName/DBlist.txt

Now create an empty file and add the following code in it.

vi convertdb.sh
#!/bin/bash

MYSQLCMD=mysql

for db in `cat /home/cPanel_UserName/DBlist.txt`; do
for table in `echo show tables | $MYSQLCMD $db | grep -v Tables_in_`; do
TABLE_TYPE=`echo show create table $table | $MYSQLCMD $db | sed -e’s/.*ENGINE=\([[:alnum:]\]\+\)[[:space:]].*/\1/’|grep -v ‘Create Table’`
if [ $TABLE_TYPE = “InnoDB” ] ; then
mysqldump $db $table > $db.$table.sql
echo “ALTER TABLE $table ENGINE = MyISAM” | $MYSQLCMD $db
fi
done
done

Now execute the script as root

sh convertdb.sh

And you are done 🙂