Europe’s striving for reduced CO2 fleet emissions of heavy-duty commercial vehicles influences futures powertrain architectures. The use of CO2-free drives as battery electric have been demonstrated for various applications. Also for HD trucks BEVs will be an important contributor to achieve the 2025 fleet targets of 15% compared to the 2019 reference. Starting with the year 2030 significantly more stringent targets will be in place, currently −45% is in discussion. This draws the attention to Hydrogen. For many manufacturers the hydrogen engine (H2 ICE) is the faster and most cost-efficient option. In the last four years AVL did conduct several performance and emission development projects on different hydrogen engines. One of the most essential project enablers has been the AVL RPEMS (rapid prototype engine management system). Its proven application software (ASW) is designed to support development of port fuel injection (MPI), direct injection (DI) and HPDI with Diesel pilot. Both steady state and transient operation is possible. It contains necessary functions to control exhaust aftertreatment systems (e.g.: single or double dosing SCR) as well. In view of series production intended EMS developments AVL does focus on maximal similarities to existing control approaches. Especially for OEM with own controls development an extension of existing functionalities to manage H2 ICE operation is most attractive compared to entirely new software structure. To test this approach AVL has extended its Diesel software (quality control) as well as its Gas software (quantity control) to operate the various H2 ICE via its RPEMS. Also a combination of standard EMS (e.g. for torque and airpath control) and AVL RPEMS for H2 injection, ignition and lambda control is possible. This allows testing of H2 ICE concepts in a very early development state on engine testbed and vehicle. Furthermore, the diagnosis of irregular combustion events like knocking, misfire, late and early pre-ignition, which sometimes occurs in combination with backfire have to be detected and the correct measures in engine control for engine protection must be performed. The article describes engine testbed results of diesel based software and comparison of both control strategies performed on a high sophisticated H2 ICE model as well as irregular combustion diagnosis and measures for engine protection.