Different ways to protect resources in a VPS

Hey guys, this question comes from a web developer who has set up some basic web servers using Linux-based VPS and protected resources through token authorization.

I'm curious to find out more and better ways of protecting the access to different resources that may live in a server so I'm interested in seeing you guys approaches to tackling this problem.

It's a question out of pure curiosity so there's no rush in solving any issues.

Thanks in advance!