Nanostructured polystyrene (PS) and polymethylmethacrylate (PMMA) were used as carriers for the preparation of bioconjugates with lipolytic enzymes, such as Candida rugosa lipase (CRL) and Pseudomonas cepacia lipase (PCL). Simple addition of the lipase solution to the polymeric nanoparticles under protein-friendly conditions (pH 7.6) led to the formation of polymer-enzyme bioconjugates. Energy filtered-transmission electron microscopy (EF-TEM) performed on immuno-gold labeled samples revealed that the enzyme preferentially binds to the polymer nanoparticles and that the binding does not affect the nanostructured features of the carriers. The studies performed on the activity of the bioconjugates pointed out that the lipases adsorbed onto polymeric nanoparticles show an improved performance in terms of activity and selectivity with respect to those shown by lipases adsorbed on the same non-nanostructured carriers. The residual activities of CRL and PCL immobilized on nanostructured PMMA and PS reached 60% and 74%, respectively. Moreover, we found that enantioselectivity and pH and thermal stability increase upon immobilization. These results highlight the fact that new protein conformers with improved enantioselectivity stabilized after adsorption on nanoparticles are obtained. On the basis of the chemical structures of the selected polymers and the slopes of the adsorption isotherms, a hydrophobic binding model for lipase/nanostructured polymers is suggested.