Both hydrogen and ammonia are potential fuels that can significantly replace fossil fuels in the automotive and energy sectors. In compression ignition engines, they can be effectively and efficiently co-combusted with diesel fuel. This study presents experimental comparative research on the impact of alternative fuels, namely ammonia and hydrogen, on the performance, stability, and emissions of an industrial dual-fuel compression ignition engine. The research was conducted on an engine operating under constant load (0.7 MPa) and constant speed (1500 rpm), comparing scenarios of diesel-only operation and alternative fuel energy shares of 8 %, 12 %, 24 %, and 32 %. For both ammonia/diesel and hydrogen/diesel engines, combustion characteristics, performance, and emissions were determined and analyzed. Additionally, an evaluation of the dual-fuel engine’s operational stability was conducted. For the compression ignition engine co-combusting ammonia with diesel, the most favorable solution was using a 32 % energy share of NH3. In this configuration, the engine achieved nearly the highest efficiency (38 %), the most stable operation, and the lowest emissions of harmful and toxic exhaust components (NO = 2.23 g/kWh, HC = 0.2 g/kWh, CO = 24.9 g/kWh, CO2 = 512 g/kWh, Soot = 0.51 g/kWh). For the engine co-combusting hydrogen with diesel, the optimal energy share of H2 was 24 %. In this configuration, the engine achieved the highest efficiency (39.8 %), almost the most stable operation, and the lowest emissions of HC = 0.22 g/kWh, CO = 15.8 g/kWh, CO2 = 434.7 g/kWh and Soot = 0.52 g/kWh. Unfortunately, a significant drawback of using H2 in a compression ignition engine is the substantial increase in NO emissions.