The problem of climate change and the reduction of fossil fuels has motivated the development of research focused on improving the efficiency of internal combustion engines. This research proposes a methodology based on mathematical models to determine the energy losses caused by auxiliary systems and friction processes in the engine. Therefore, models are proposed for calculating the energy losses in fuel injection, lubrication, and cooling system. In the same way, models are proposed for the energy losses due to friction in the piston, valve train, and bearings. Experimental tests are carried out on a single-cylinder diesel engine under different operating conditions to validate the proposed models. The results showed that the energy losses of the fuel injection, lubrication, and coolant system are equal to 0.61%, 0.30%, and 0.31% of the chemical energy of the injected fuel. In the case of the energy losses by friction processes, the piston, valve train, and bearings represent 5.47%, 1.34%, and 1.85% of the fuel energy, respectively. Additionally, the proposed model allows estimating the minimum lubrication film present in the piston, valve train, and bearings, which in the particular case of the present study were 0.63 µm, 0.10 µm, and 0.57 µm, respectively. In general, the methodology developed in the present work stands as a robust tool to evaluate the modifications and/or designs of auxiliary systems and friction processes to reduce the energy losses and protect the system from wear caused by lubrication problems. Additionally, the methodology allows evaluating the effect of different types of fuels on the lubrication conditions of the piston and the crankshaft bearings.