Abstract The use of biogas in internal combustion engines presents many advantages. Nevertheless, the CO2 content in the fuel negatively affects the combustion process, reducing combustion speed and stability. The presence of hydrogen in the biogas would improve its combustion characteristics. This paper investigates the combustion of biogas in a Controlled Auto Ignition (CAI) engine by means of numerical simulations. A model of the combustion system was developed for analyzing the use of biogas in a Chemkin environment. The biogas considered in this paper naturally contains hydrogen as a result of a new anaerobic digestion process. The CAI internal combustion engine model allowed the evaluation of engine performance and emissions. Different hydrogen contents were investigated to find the optimal fuel composition for reducing nitrogen oxides emission. Exhaust Gas Recirculation (EGR) was adopted for controlling in-cylinder temperature and therefore fuel auto-ignition. In fact, the presence of very reactive chemical species in the EGR, such as nitric oxide (NO), resulted to have an important impact on the onset of combustion. The results demonstrated that biogas containing hydrogen allow a reduction of NOx emissions with respect to a conventional biogas. An optimal biogas composition was identified, allowing a 32% reduction in NOx emission compared to the conventional biogas. The reaction mechanism for NO formation did not change with biogas composition, with an important contribution coming from prompt NOx formation mechanism. The main differences were in the reaction rates, higher for the conventional biogas.