Please follow the steps to remove the Let's Encrypt SSL Certificate: First take a backup of letsencrypt directory under /etc - sudo cp -r /etc/letsencrypt/ /etc/letsencrypt.backup I deleted the ‘no longer needed domains’ in the three folders… rm -rf /etc/letsencrypt/live/${DOMAIN} rm -rf /etc/letsencrypt/renewal/${DOMAIN}.conf rm -rf /etc/letsencrypt/archive/${DOMAIN}