Agreed with @ahaw021, since we don't offer wildcard certificates, this will definitely be more complex. By default you would run into rate limit problems because Let's Encrypt allows only 100 names per certificate and limits the number of certificates you can issue per week that apply to the same top-level domain.
If you are a hosting provider hosting these on behalf of customers, you may be able to get a rate limit exemption. See
Various hosting providers have managed to get this to work; it would definitely require some programming effort, though.
If you're not a hosting provider, I don't think Let's Encrypt can handle your situation properly because the rate limits will prevent you from issuing a large enough number of certificates to cover all of your subdomains.