In this short story, I will share my experience about using the Let’s Encrypt SSL certificate for cPanel hostname. As you know, cPanel provides a free SSL certificate for cPanel hostname as default. But some times it now works for Iranian domain, so you can use the following steps to have a valid SSL certificate for your cPanel services.

Install the Certbot from EPEL

Run following command to install certbot from epel repo

yum install --enablerepo=epel certbot

Create deploy-hook script for Certbot

Create file

vim /usr/local/bin/
# Copy following lines on it
set -e

/bin/cat /etc/letsencrypt/live/$HOSTNAME/privkey.pem /etc/letsencrypt/live/$HOSTNAME/cert.pem > /var/cpanel/ssl/cpanel/cpanel.pem
/bin/chown cpanel:cpanel /var/cpanel/ssl/cpanel/cpanel.pem

/bin/cat /etc/letsencrypt/live/$HOSTNAME/privkey.pem > /var/cpanel/ssl/exim/exim.key
/bin/cat /etc/letsencrypt/live/$HOSTNAME/cert.pem > /var/cpanel/ssl/exim/exim.crt
/bin/chown mailnull:mail /var/cpanel/ssl/exim/exim.*

/bin/cat /etc/letsencrypt/live/$HOSTNAME/privkey.pem > /var/cpanel/ssl/ftp/ftpd-rsa-key.pem
/bin/cat /etc/letsencrypt/live/$HOSTNAME/cert.pem > /var/cpanel/ssl/ftp/ftpd-rsa.pem
/bin/cat /etc/letsencrypt/live/$HOSTNAME/privkey.pem /etc/letsencrypt/live/$HOSTNAME/cert.pem > /var/cpanel/ssl/ftp/pure-ftpd.pem
/bin/chown root:wheel /var/cpanel/ssl/ftp/*

/bin/cat /etc/letsencrypt/live/$HOSTNAME/privkey.pem > /var/cpanel/ssl/dovecot/dovecot.key
/bin/cat /etc/letsencrypt/live/$HOSTNAME/cert.pem > /var/cpanel/ssl/dovecot/dovecot.crt
/bin/chown root:wheel /var/cpanel/ssl/dovecot/dovecot.*

/bin/systemctl restart cpanel.service
/bin/systemctl restart exim.service
/bin/systemctl restart pure-ftpd.service
/bin/systemctl restart dovecot.service

Now make it executable

chmod +x /usr/local/bin/

Issue a certificate for cPanel hostname

With the following command you will be able to issue a Let’s Encrypt valid certificate for cPanel HOSTNAME

certbot --debug certonly -a webroot --agree-tos --webroot-path=/usr/local/apache/htdocs --deploy-hook=/usr/local/bin/ --renew-by-default -d $HOSTNAME

Certificate renew cron job

For the certificate, auto-renew add the following cron job

00 02 * * * certbot renew

Source: cPanel Forums