Abstract Two process solutions were proposed for biochemical reactions carried out in the biphase organic solvent–water system where a membrane played the role of sustaining an interface. One of the two solutions with a passive- or active-type membrane was selected on the basis of the kinetic or diffusional regime of a particular process. Enzymatic synthesis of ZAlaPheOMe, the precursor of bitter dipeptide was discussed. On the basis of analysis of relative rates of enzymatic conversion and extraction of hydrophobic (a limiting substrate)—ZAlaOH from organic to aqueous phase, the range of the process was determined using the Hatta model. Very low values of the Hatta number were obtained which indicated that the process was carried out in the kinetic regime. Such a process solution was selected in which the enzyme was dissolved in the whole volume of the aqueous phase (passive character of the membrane). The process of ZAlaPheOMe synthesis confirmed a proper choice of the process solution; during the process the substrate concentrations in the aqueous phase were close to equilibrium concentrations. An intensive extraction of a hydrophobic product to the organic phase and high stability of the applied catalyst were observed.