The article describes the methodology of engine tests on new types of low-sulphur marine fuels in laboratory conditions in order to conduct a comprehensive assessment of their suitability for powering full-size marine engines. The innovativeness of the proposed solution consists of adapting the laboratory Diesel Engine Test Bed to carry out experimental tests using residual and alternative fuels so that it is possible to imitate the real operating conditions of the ship engine. The main aim of the research program was to assess the energy efficiency of six different low-sulphur marine fuels and their impact on the chemical emissivity of engine exhaust gases and air pollution with toxic and harmful chemical compounds. In order to achieve the research purpose formulated in this way, it was necessary to: (1) equip the constructed laboratory stand with highly specialised measuring equipment and (2) develop a technology for determining diagnostic parameters representing the basis for developing a ranking of the energy and emission quality of the tested marine fuels according to the proposed physical model. The model distinguishes 10 diagnostic parameters that, after normalisation, form two subsets of evaluation parameters - stimulant and destimulant. Determining their values made it possible to estimate a synthetic variable, according to which all the tested fuels were adjusted in the order from the “best” to the “worst”, in accordance with the adopted qualitative criteria of such an assessment. The results of the laboratory tests show that among the considered fuels, i.e., MDO, MGO, RMD 80/L, RMD 80/S, RME 180, and RMG 380 type, the best solution is to use MDO distillate fuel to power full-size marine engines. However, taking into account its high purchase price, a rational alternative decision is to choose RMG 380 type residual fuel, which ranks second in the ranking of the functional quality of the tested marine fuels.