Talk:Don’t Starve Together Dedicated Servers/@comment-25995291-20150128153916/@comment-96953-20150128211016

Actually, I don't think it's possible to specify per-instance configs for mods yet. (I'm assuming you mean that you want to run, for example, mods A and B on server 1, and mods C, D, and E on server 2, or you want to run mod F with two different configurations for servers 1 and 2.)

This might be a bit wasteful, but you can probably just make a copy of the Don't Starve Together dedicated server files into another directory, configure your alternates, and run it from there.