Easier than I thought (all stuff as SU or using SUDO):

First we need to install some Mysql-Munin perl libraries:

apt-get install libipc-sharelite-perl

Also some Perl stuff will be needed:

perl -MCPAN -eshell
install IPC::ShareLite

Next let’s activate Munin Mysql plugin:

# Assuming you have already installed both munin & mysql
ln -s /usr/share/munin/plugins/mysql_* /etc/munin/plugins

Create a user for a Mysql database (so Munin will be able to get stats as this user):

mysql> CREATE USER `munin` @`localhost` IDENTIFIED BY 'somepassword';
mysql> GRANT SUPER ON *.* TO `munin` @`localhost`;
mysql> FLUSH PRIVILEGES;

Edit /etc/munin/plugin-conf.d/munin-node file and find [mysql*] section:

[mysql*]
user root
env.mysqlopts --defaults-file=/etc/mysql/debian.cnf
env.mysqluser munin

Let’s also disable WARN: MySQL InnoDB free tablespace information (in most cases it is not valid):

Create a file /etc/munin/plugin-conf.d/mysql_innodb and place following lines into it:

[mysql_innodb]
env.warning 0
env.critical 0

or if You don’t need InnoDB part, just turn it off by removing the symlink:

rm /etc/munin/plugins/mysql_innodb

Restart both Apache & Munin:

/etc/init.d/apache2 restart
/etc/init.d/munin-node restart
su munin -c /usr/bin/munin-cron

Wait until charts regenerate and You’re ready to go! Example (generated for the first time):