The easy way: the Mods tab
- Put your factorio.com username and token in Server Settings: the mod portal only lets an account download mods. The token is on your profile at factorio.com.
- In the Mods tab, search the portal and Add each mod. Its dependencies are added for you, at releases for the server's version.
- Press Apply and restart. The server downloads the mods, restarts, and the tab tells you if Factorio refused one, with a button to put the previous mods back.
From your own game
A mod that is not on the portal goes in by hand: upload its .zip into mods with the Files tab and restart. Factorio loads a mod it finds there by default; the Mods tab lists it, to turn off or remove.
What players download
When a player joins a modded server, Factorio compares their mods with the server's and offers to download and enable the same set from the mod portal. Players need a factorio.com account for that, which every Steam copy has.
Versions
A mod is built for a version of Factorio. When the server moves to a new release, update the mods that need it the same way you added them.
Frequently asked questions
Where do Factorio server mods go?
In the mods folder, next to mod-list.json, which says which of them are enabled. On Flux the Mods tab manages that list for you; the files are in mods/ in the Files tab.
Do Space Age's mods count as mods?
They are listed in mod-list.json as space-age, quality and elevated-rails, but they come with the server; the Space Age setting turns them on or off.