Indeed, at the moment most of the software is very *nix orientated.
To help you understand, the proces of getting a Let’s Encrypt certificate is described here: https://letsencrypt.org/how-it-works/
In short, you need some soft of “client” which communicates with Let’s Encrypt issuance server through the ACME protocol. The most logical choice would be a client running on the machine on which the certificate will be used, but that isn’t 100 % necessary. For example, the list of clients referenced above also lists a few browser-based clients. Do not however, with browser based clients who will calculate the private key for you, you can never be 100 % sure the private key isn’t leaked, unless you’ll carefully scrutinise all the code of the website and make sure no serverside code is used for the private key generation nor should it ever be send to the server of the browser based client.