If you have the environment variable
XDG_DATA_HOME set, the installation is located at
$XDG_DATA_HOME/letsencrypt. Otherwise, it is located at
~/.local/share/letsencrypt. You can simply delete this directory. You can also delete configuration, work, and log directories which by default are stored at
/var/log/letsencrypt respectively. The directory where you cloned our git repo can also be deleted.
Let’s Encrypt also installs some OS dependencies and how you remove these would be very OS specific. To see what dependencies were installed, take a look at the files in the bootstrap folder at the root of our git repo (link). Take a look at the shell script for your OS to see what packages are required. You can uninstall these packages through the normal means of your OS, but make sure they aren’t required by any other programs on your system.
Source: Uninstalling letsencrypt – Let’s Encrypt Community Support