The basic way for systemd to stop a running service is by sending the SIGTERM signal (a regular kill) to the process control group of the service, and after a configurable timeout, a SIGKILL to make things really go away if not responding. Of course, all the details are configurable, and often times you’d have some sort of control script which did the actual stopping, but I am only talking about the simple case here. I have a Java-based service and a Unit configuration file to integrate it with systemd. The JVM process is setup so that it gracefully shuts down the service upon reception of the SIGTERM signal (using shutdown hooks). However, the JVM will still exit with code 143 in the end due to receiving SIGTERM (128+15), and systemd thinks something went wrong when stopping the service. The solution is simple: add SuccessExitStatus=143 to the Unit configuration file for the service, and systemd will consider this code as successful termination. If the graceful shutdown can take some time, add TimeoutStopSec=NN as well to give the service process more time before systemd brings out the big gun.
Relevant manual pages: systemd.kill and systemd.service.