Based on the experimental results and model simulation it was shown that Bi-Bi Ping Pong mathematical process model is not suitable for the description of the lipase catalysed biodiesel production in a microreactor. Therefore, three additional mathematical process models were proposed. Prior to transport model development, the reaction rates were described with double substrate Michaelis-Menten kinetics, Bi-Bi Ping-Pong kinetics, and Hill kinetics. The Hill kinetic model was proposed as the best kinetic model based on the model selection criterion. In order to validate the proposed mathematical process models, biodiesel synthesis in a microreactor was performed at four different initial process conditions. In all validation experiments, free fatty acid concentration and enzyme concentration were kept constant and the oil to methanol ratio in the inlet streams was altered. An increase of biodiesel yield was observed for the higher methanol concentration in the system. If a large excess of methanol was used (oil to methanol ratio 1:90) the yield was higher than 90% for the residence time of only 40 min. In comparison to the batch process, where the yield of 96% was achieved for 48 h, this was a significant improvement. Two out of three proposed mathematical process models described experimental data very well for all analysed residence times. Considering the level of complexity and accuracy, a mathematical process model of steady-state two parallel plug flow reactors was proposed as the optimum solution for the mathematical description of enzymatic biodiesel synthesis performed in a microreactor.