To substitute fossil fuels, biodiesel can be produced from vegetable oils, animal fats, and waste cooking oils by transesterification with ethanol. This reaction, generally conducted in batch reactors, leads to high conversion of triglycerides into ethyl esters with diglycerides and monoglycerides as reaction intermediates and glycerol as by-product. Function of the scheme and the thermokinetic properties of the system, continuous processes may withdraw existing obstacles of batch processes such as the large number of steps, secondary reactions, stable equilibria and difficulties to separate the products. This system is complex due to phase equilibria and important coupling of phenomena (reaction, mixing, heat and mass transfers). Hence, to properly design a continuous process, numerous data are required. In this work, we transferred the batch reaction into a continuous microstructured device, which induces a better control of heat and mass transfers. Furthermore, it enables us to perform the reaction with small amounts of reactants to screen the operating conditions. The results show that reaction and separation can be carried out consecutively or simultaneously in microreactors and products can be obtained with higher purity. Continuous processes would reduce ethyl esters production costs.