Abstract Biodiesel can be produced from vegetable oils using different catalysts including enzymes. This publication presents the development of a mathematical model for biodiesel production using the liquid lipase Callera Trans L (CTL) and analyzes the first block of reactions: esterification of free fatty acids (FFA) in biodiesel and hydrolysis of the latter. The relevant rate constants were evaluated by changing water, methanol, FFA and enzyme concentrations. The results were compared to the immobilized catalyst Novozym 435 (Nvz). The intriguing difference was observed for the apparent equilibrium constants of CTL (high K eq app ) and Nvz (low K eq app ). This thermodynamic “inconsistency” was explained by absence or presence of the catalyst carrier. Nvz carrier particles apparently help to disperse water, increasing its surface and hydrolytic activity in comparison to CTL. Another reactant, methanol, had a dual effect acting as (i) a substrate and (ii) a solvent of water in oil phase. The latter effect added to hydrolytic activity and decreased K eq app at increasing methanol (0–0.5 M). Inhibition and inactivation of CTL by methanol ( 1.5 M.