I recently installed mopidy on debian through the apt repository. But when I start the service using systemctl or mopidyctl it will not use the config in my ~/.config/mopidy, even though I changed the config to use in the .service file under /lib/systemd/system/mopidy.service. When I start the server manually (from the terminal simply using “mopidy”) everything works fine
This is by design and follows the conventions of most Debian-packaged services. See https://docs.mopidy.com/en/latest/debian/ for details.
You want to install mopidy as a user service in that case. Put the unit file under ~/.config/systemd/user and enable with systemctl --user command.
You do not need to use the User= declaration in this case since it will be set automatically.