In the present paper, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) nanocapsules were prepared by a double emulsion-solvent evaporation procedure (w/o/w) for the encapsulation of model enzymes (L-asparaginase, catalase, glucose oxidase) and bovine serum albumin. To increase the encapsulation efficiency and activity of the encapsulated enzyme, numerous modifications were made in the compositions of the phases of double emulsion. For the preparation of low molecular weight PHBV, the polymer was treated with sodium borohydride. A 14-fold decrease in molecular weight (from 297 000 to 21 000) was observed upon 4 h of incubation. Although the amount of encapsulated protein was not increased, the enzyme activity increased upon use of low molecular weight PHBV, indicating that these nanocapsules have a higher permeability to solutes (reactants and products). The adjustment of the second water phase to the isoelectric point of the proteins significantly increased the encapsulation yields of catalase, L-asparaginase and BSA. Likewise, polyethylene glycol coupling significantly increased the entrapment efficiency as well as the activity of catalase and L-asparaginase. A combination of the various optimum preparation conditions further increased the encapsulated catalase activity (about sixfold) in comparison to the initial basic conditions (with no modification and no isoelectric point adjustment).