The article discusses the problem of replacing traditional diesel fuel with an alternative one. Rapeseed oil is considered as an alternative motor fuel. A deterioration in the quality of injection and atomization processes was noted when converting the engine to rapeseed oil. Experimental studies of the MD-6 diesel engine have shown that it can operate effectively on both petroleum diesel fuel and rapeseed oil. At the same time, the transfer of this engine from petroleum diesel fuel to rapeseed oil was accompanied by an increase in brake-specific fuel consumption, an increase in exhaust gas opacity, and an increase in emissions of nitrogen oxides and carbon monoxide. These negative phenomena are partly eliminated by adjusting the fuel injection advance angle. Improved engine performance is also achieved by optimizing the characteristics of the fuel supply system and two-phase fuel supply. The implementation of these measures makes it possible not only to achieve the performance of a diesel engine characteristic of running on diesel fuel, but also to meet the requirements for fuel efficiency and exhaust gas toxicity that are promising for small-sized high-speed diesel engines.