The kinetics of the tryptic release of bioactive peptides from caseinomacropeptide was investigated in both batch and continuous mode in an enzymatic membrane reactor. The hydrolysis of the three susceptible bonds, Lys(111)-Lys(112), Lys(112)-Asn(113), and Lys(116)-Thr(117), was monitored by quantitative determination of the released products. A kinetic study in the batch system showed that the overall catalytic process follows a sequential mechanism where the Lys(116)-Thr(117) bond was only cleaved on the intermediary products resulting from the cleavage of the Lys(111)-Lys(112) and Lys(112)-Asn(113) bonds. When the reaction was performed in the continuous enzymatic membrane reactor, it was found that the enzyme preference toward the Lys(116)-Thr(117) bond depended on the relative concentrations of both the caseinomacropeptide and the intermediary products accumulated at steady state. Such concentrations were controlled by the enzyme and substrate concentrations and the substrate feeding flow rate; hence, by control of the operating parameters and with the understanding of the reaction mechanism, the enzyme action toward various peptidic bonds can be oriented in the continuous mode, offering the possibility of better control of the type of product recovered in the reactor output.