For Apache, in the folder sites-available, you need to create your the-new-one.your-domain.com.conf file. Then enable the new site with a2ensite the-new-one.your-domain.com. Now we add the SSL using certbot. You need to list all the existing domains and add the new one: certbot –apache –cert-name your-domain.com -d first.your-domain.com,second.your-domain.com,third.your-domain.com,the-new-one.your-domain.com