A recombinant aminopeptidase (90 kDa) of Lactobacillus rhamnosus S93 produced by E. coli was encapsulated in alginate or chitosan-treated alginate beads prepared by an extrusion method. This study investigated the effects of alginate, CaCl2, chitosan concentrations, hardening time, pH and alginate/enzyme ratios on the encapsulation efficiency (EE) and the enzyme release (ER). Chitosan in the gelling solution significantly increased the EE from 30.2% (control) to 88.6% (coated). This polycationic polymer retarded the ER from beads during their dissolution in release buffer. An increase in alginate and chitosan concentrations led to greater EE and lesser ER from the beads. The greatest EE was observed in a pH 5.4 solution (chitosan-CaCl2) during bead formation. Increasing the CaCl2 concentration over 0.1 M neither affected the EE nor the ER. Increasing hardening time beyond 10 min led to a decrease in EE and the alginate:enzyme ratio (3 : 1) was optimal to prevent the ER.