Carbon-free mobility is becoming increasingly important today. For long-distance transportation or off-road applications with high power demand, the combustion engine remains a good option. To achieve a fast greenhouse gas reduction, hydrogen as a carbon-free fuel is an economically and ecologically suitable solution. One of the biggest challenges for a hydrogen engine is its safe and reliable operation. For instance, the hydrogen concentration outside of the combustion chamber must be kept at a very low level during operation. From a software perspective, diagnostic functions, that monitor the correct functioning of all valves and injectors are required, in combination with an advanced leak monitor, to detect potential leaks at an early stage. In addition, the software must help to protect the mechanical parts to ensure a long lifetime. For hydrogen engines, back-fire, knocking combustion and pre-ignition are high-risk factors. The software presented in this publication detects these phenomena and enables hydrogen-specific countermeasures such as cylinder individual adjustment of the A/F ratio in combination with adjustment of the ignition angle. Other main problems occur during system startup and shutdown. For a save and successful engine start, the risk of combustion of undefined hydrogen mixtures from previous engine shutdowns as well as the water condensation must be prevented. As with the refueling process, the interaction with the tank software must also be taken into account here. All these functions are integrated into the FEV hydrogen control software and have been tested on different applications. The presentation highlights the main challenges for the safe operation of a hydrogen engine and presents both the required software solution and the corresponding measurement results.