Intro:
Since a while now the wonderful idea of creating the service Letsencrypt has made lots of admins happy.
Here is how we can also use Letsencrypt with ISPConfig 3.1.

Ref: https://www.howtoforge.com/community/threads/ssl-how-to-for-ispconfig-3-with-letsencrypt.74738/

STEPS:
Define ISPconfig to use the new SSL certificate with symbolic links.
(If you don’t know how to use symbolic links this how-to is not for you)
/usr/local/ispconfig/interface/ssl/
ispserver.crt -> /etc/letsencrypt/live/mydomain.com/fullchain.pem
ispserver.key -> /etc/letsencrypt/live/mydomain.com/privkey.pem

Define Postfix to use the new SSL certificate in /etc/postfix/main.cf.
(If you don’t know how to add these entries this how-to is not for you)
smtpd_tls_cert_file = /etc/letsencrypt/live/mydomain.com/cert.pem
smtpd_tls_key_file = /etc/letsencrypt/live/mydomain.com/privkey.pem
smtpd_tls_CAfile = /etc/letsencrypt/live/mydomain.com/fullchain.pem

Define Dovecot to use the new SSL certificate in /etc/dovecot/dovecot.conf.
(If you don’t know how to add these entries this how-to is not for you)
ssl_cert = </etc/letsencrypt/live/mydomain.com/fullchain.pem
ssl_key = </etc/letsencrypt/live/mydomain.com/privkey.pem

# Restart/reload the services involved
sudo service postfix reload
sudo service dovecot reload
sudo service apache2 restart