Your multi-domain cert will be in the folder named with the first -d supplied flag.
For example, let’s say you requested your cert with the following command:
letsencrypt certonly --webroot --webroot-path /var/www/html -d me.domain.org -d domain.org -d mail.domain.org -d www.domain.org -d domain.net -d mail.domain.net
You will find your certificate, private-key in the folder /etc/letsencrypt/archives/me.domain.org and the files in /etc/letsencrypt/live/me.domain.org will point to the latest certificate issued.