An approach for controlled protein immobilization on laser-induced two-photon (2P) oxidation patterned graphene oxide (GO) surfaces is described. Selected proteins, horseradish peroxidase (HRP) and biotinylated bovine serum albumin (b-BSA) were successfully immobilized on oxidized graphene surfaces, via non-covalent interactions, by immersion of graphene-coated microchips in the protein solution. The effects of laser pulse energy, irradiation time, protein concentration and duration of incubation on the topography of immobilized proteins and consequent defects upon the lattice of graphene were systemically studied by atomic force microscopy (AFM) and Raman spectroscopy. AFM and fluorescence microscopy confirmed the selective aggregation of protein molecules towards the irradiated areas. In addition, the attachment of b-BSA was detected by a reaction with fluorescently labelled avidin-fluorescein isothiocyanate (Av-FITC). In contrast to chemically oxidized graphene, laser-induced oxidation introduces the capability for localization on oxidized areas and tunability of the levels of oxidation, resulting in controlled guidance of proteins by light over graphene surfaces and progressing towards graphene microchips suitable for biomedical applications.