In the last years, there has been an increasing interest in controlling the protein adsorption properties of surfaces because this control is crucial for the design of biomaterials. On the other hand, controlled immobilization of proteins is also important for their application as solid surfaces in immunodiagnostics and biosensors. Herein we report a new protein patterning method where regions of the substrate are covered by a hydrophilic film that minimizes protein adsorption. Particularly, poly(vinyl alcohol) (PVA) cross-linked structures created by an especially developed photolithographic process are proved to prevent protein physisorption and they are used as a guide for selective protein adsorption on the uncovered areas of a protein adsorbing substrate such as polystyrene. The PVA cross-linking is induced by photo-oxidation using, as a catalyst, polyoxometalate (H3PW12O40 or α-(NH4)6P2W18O62), which is removed using a methyl alcohol/water mixed solvent as the developer. We demonstrate that the polystyrene and the cross-linked PVA exhibit dramatically different performances in terms of protein physisorption. In particular, the polystyrene areas presented up to 130 times higher protein binding capacity than the PVA ones, whereas the patterning resolution could easily reach dimensions of a few micrometers. The proposed approach can be applied on any substrate where PVA films can be coated for controlling protein adsorption onto surface areas custom defined by the user.