The use of ammonia as an alternative fuel in automotive industry is not yet fully established; further research and development are required that need to account for both engine and aftertreatment systems as well as their integration and control to ensure most efficient use of ammonia. In this work we present a fully physical and chemical-based toolchain for co-simulating ammonia and biodiesel fuelled compression ignition engine with selective reduction catalysts (SCR) for exhaust aftertreatment. The investigations refer to experimental data from a single-cylinder research engine. This is a direct injection engine that was retrofitted to run on ammonia and biodiesel, the latter acting as a combustion promoter. Engine in-cylinder processes were simulated using a stochastic reactor model. Detailed gas phase chemistry is used to simulate the combustion process and pollutants formation. The SCR aftertreatment model employs detailed surface chemistry that is trained using available data from literature. Eventually, the co-simulation toolchain was applied to investigate numerically the impact of the properties of the catalyst on ammonia reduction under engine operating conditions.