Synthesis of biodiesel fuel by enzymatic methanolysis of vegetable oil is promising because of the indifference of such a process to the quality of the feedstock. In order to reduce costs, it is convenient to use as the catalyst immobilized cells of lipolytic microorganisms, without separation of pure lipases. We studied methanolysis of sunflower oil in a continuous flow reactor and a stirred tank reactor when using immobilized Aspergillus niger mycelium and Yarrowia lipolytica cells, both free and immobilized, as the catalyst. In the continuous flow reactor, up to 62.2% yield of fatty acid methyl esters is achieved when using Aspergillus niger cells.