Excessive exploitation and rise in price of fossil fuels have stimulated more intensive research into the production of alternative fuels such as biodiesel. One of the possible solutions for biodiesel production process, is the enzyme-catalyzed transesterification of oils or fats in the presence of simple alcohols. A step forward in the development of the biodiesel production process, in terms of intensification of mass and energy transfer and the consequent increase in the overall apparent reaction rateand reduction in reaction time is the use of microreactor systems. In order for the biodiesel production process to be fully sustainable and industrially applicable, the enzyme must be stabilized and used in multiple production cycles. One way to preserve enzymatic activity is to replace conventional buffer solutions with Natural Deep Eutectic Solvents (NADES). In this research, biodiesel was produced by the process of transesterification catalyzed by the lipase enzyme derived from Aspergillus oryzae. The first step in replacing conventional solvents with green solvents was to test the enzyme activity in NADES betaine:urea 1:3 with 40% (w/w) water. The volume activity of the lipase enzyme proved to be the highest after the lipase was extracted directly in NADES betaine:urea 1:3 with 40% (w/w) water. After extraction, biodiesel synthesis was carried out in a batch reactor, a membrane reactor and a microreactor. In experiments with a molar ratio of oil:methanol of 1:90 in a batch reactor, a yield of 99% was obtained after 30 hours of synthesis. After completion of the synthesis, the biodiesel was separated from the reaction mixture and the enzyme was used again for biodiesel synthesis. Three cycles of biodiesel synthesis were successfully carried out without the addition of a new enzyme, with a total duration of 216 hours.