Bast, the way I understand it is that Let's Encrypt is not a Root Certificate Authority, it's an intermediate. The root CA of Let's Encrypt is " DST_Root_CA_X3.crt", you should find it in /etc/ssl/certs/. I have sucessfully installed a Let's Encrypt certificate on a debian machine by Octobre 2016th too and it worked just fine. -- Yassine.