Some parameters of the emulsion polymerization process were studied in order to optimize the incorporation of the enzymes l-asparaginase (l-ASNase) and superoxide dismutase (SOD) into polyisobutylcyanoacrylate (PIBCA) nanoparticles and to make a contribution to the characterization of enzyme-loaded nanoparticles. Optimization criteria were the maximization of enzyme load and the minimization of the lost of catalytic activity. The effect of enzyme molecular weight, enzyme concentration and enzyme substrate on the loading performances were studied and discussed considering the mechanism of emulsion polymerization. The effect of the polymerization process on the characteristics of immobilized l-ASNase and SOD, macromolecules with very different three-dimensional structures, were studied. The incorporation of enzymes in PIBCA nanoparticles must be strongly dependent on the enzyme structure. The performances of the incorporation of SOD in PIBCA nanoparticles can be compared with results regarding other colloidal carriers.