WHM Certificates Are not Working

4

i see your problem you need 2 separate certs for

or 1 cert with 2 webroot paths

  • mainserver.mydomain.com where web root path for cpanel main host name is usually off /usr/local/apache/htdocs unless you created that as a new site account in whm then it would also be /home/anotherusername/public_html
  • mydomain.com where web root path for cpanel is /home/username/public_html

so based on webroot manual documentation at https://letsencrypt.readthedocs.org/en/latest/using.html#webroot you would need a command similar to one outlined at https://forums.cpanel.net/threads/how-to-installing-ssl-from-lets-encrypt.513621/ using non-letsencrypt-auto command instead

cd /root/.local/share/letsencrypt/bin/
./letsencrypt --text certonly --renew-by-default --webroot --w /home/username/public_html -d mydomain.com \ 
-w /usr/local/apache/htdocs -d mainserver.mydomain.com

where mainserver.mydomain.com webroot is either /home/anotherusername/public_html or /usr/local/apache/htdocs