The synthesis of the protected dipeptide BocGly-PheOMe has been carried out in an aqueous-organic two-liquid-phase system. The reaction has been catalyzed by the pretense papain using trichloroethylene as organic phase with an organic phase-aqueous phase volume ratio, V-org/V-aq, of 4. The results of the present article can be summarized as follows : a) A relationship between enzyme deactivation, interfacial area, and interfacial tension is stated. The addition of 0.4% Tween 80 to the reaction system stabilized papain activity for > 50 h, overcoming the problems related to the presence of the organic solvent and shear stress due to mixing; b) undesirable parallel reactions are identified; c) the peptide yield was increased by working with a fed-batch strategy.