This article presents the authors’ considerations regarding the possibilities of developing fuel equipment for modern compression ignition engines used in special and non-road vehicles. The paper discusses the process of fuel combustion and atomization in the chamber of a piston combustion engine. The paper then presents the concept of modifying the atomizer of a modern fuel injector for operation using hydrogen-containing fuels of plant origin. The authors present a review of tests performed using an engine dynamometer on a modern engine with a Common Rail system running on biofuel. The CI engine operated with standard and modified fuel injectors. During the tests, the external ecological characteristics of the engine were analyzed as a function of rotational speed; the values of injection doses at individual rotational speeds and their effects on the characteristics were read from the current parameters, and the pressure and temperature in the engine’s combustion chamber were measured. The research results show that implementing the changes proposed by the authors of this work is a good direction for the development of compression ignition engines.