A protein-direct synthetic route to make nanobiohybrids containing copper nanoparticles (CuNPs) using an enzyme in combination with copper sulfate in aqueous media at room temperature is described. Enzyme–Cu(II) intermediates, rapidly generated in aqueous media, are transformed, induced by the enzyme structure, to facilitate the formation of a particular Cu species, tailoring the size of the nanoparticles formed depending on the experimental conditions, e.g. the pH, reducing step, amount of enzyme or incubation time. This controlled synthesis allows the preparation of tailor-made nanobiohybrids of Cu(0)NPs, Cu(0)/Cu₂ONPs, Cu₂ONPs or Cu₃(PO₄)₂NPs on the multimilligram scale. The catalytic performance of the novel CuNPs nanobiohybrids was evaluated in relation to the selective C–H functionalization of benzene via direct monohydroxylation using hydrogen peroxide as a green oxidant under mild conditions, in aqueous media and at moderate temperature. Optimization of the amount of hydrogen peroxide, the co-solvent, and the temperature was performed, resulting in the production of 17 mM phenol with 83% selectivity using the Cu-CALB-PHOS-NR nanobiohybrid as a catalyst.