Is this a bad way to store user generated CSS changes?

I'm building a website within a small agency that allows our clients to modify their basic CSS file by a GUI. So if the user changes the font-family, we do the following process:

User signs up: we create a directory based on the user's domain name (john), within our users directory on the server, then we place a index.html (template) and then styles/main.css. Once the user makes an css edit we write it to main.css

Is this a good idea? writing to the disk all the time and storing a folder for each user (linux based server)? Or is there a better way to store the CSS edits? Maybe within a database but still I would run into the issues of storing the CSS for each file.

I don't want to use inline CSS either (this would be a lot easier obviously).

I just feel like this is a bad way to do so... maybe I'm just over thinking this?

Note: current stack we are using: Node/Express/Mongo.