This paper presents a method of production and properties of ethyl esters as well as the differences between them and methyl esters. It discusses the technology of esterification and the benefits brought by the use of rapeseed ethyl esters as renewable fuel. It also presents elements of structure, actuators and control mechanisms of a mobile biodiesel production plant, owned by the Department of Mechatronics, University of Warmia and Mazury. An algorithm of a transesterification process is presented along with algorithms of a flow-through process control and the possibilities of their automation. The benefits of applying such a solution are also discussed.