New nanoparticles are synthesized through emulsion polymerization, using distinct comonomers (styrene, divinylbenzene, glycidyl methacrylate and pentafluorostyrene). Then, for the first time, two strategies are adopted to functionalize such nanoparticles using benzylamine and thiophenol: (i) after the manufacture of the nanoparticles; and (ii) in situ during the polymerization reaction. Afterwards, the functionalized nanoparticles are used as nanosupports for immobilization of lipase B from Candida antarctica and the performance of the novel nanobiocatalysts are evaluated. It is shown that the nanoparticles exhibit different properties (specific areas ranging from 34 m2 g−1 to 324 m2 g−1; and contact angles ranging from 29° to 126°), indicating that both procedures can be used to adjust the properties of the polymer supports. Moreover, the nanobiocatalysts are applied successfully in hydrolysis and esterification reactions, exhibiting higher activities than the non‐functionalized biocatalysts. It is also observed that more hydrophilic supports result in more active biocatalysts in hydrolysis (27 ± 1 U g−1) and intermediate hydrophobic matrices conduct to more active biocatalysts in esterification reactions (1564 ± 50 U g−1). It is shown that highly hydrophobic surfaces may cause a significant decrease in the activity of such biocatalysts, probably due to distortions on the enzyme active center and to more intense chemical partitioning effects.