Chromium’s (Chrome’s) protocol handling works in a different way then Firefox does. Firefox has it’s own piece of code to handle it (and configure it). Chromium uses xdg-utils to see what it needs to do.
You need to first find out the .desktop file of the application that you want to open when you click on a “magnet:” link. So go to /usr/share/applications and find you applications’ filename. In my case it was “qBittorrent.desktop”
Now we tell xdg-open that it should open up qBittorent when you click a link with the mime type “x-scheme-handler/magnet”. Like so:
xdg-mime default qBittorrent.desktop x-scheme-handler/magnet