It's absolutely possible. Don't do it.
Godot is a games engine, that's what it's built for, that's what it's good at. Using it to make a non-gaming server is going to mean you creating absolutely everything from scratch. Please don't do this to yourself. Assuming this is online, use something like a python django (REST) framework (or other language / framework of your choice depending on your project specs) which is built for precisely this sort of thing, already has exquisite architecture, a thousand tutorials, where you've got every library imaginable and cutting edge security features built in. Take the ferry with everyone else, don't get into the rubber dingy on your own. When you want to make a game, use Godot.