Ar⁺ ion sputtering on pyrite surfaces leads to the generation of sulfur vacancies and metallic iron. Our research shows that sputtering and annealing processes drive electrostatic changes on the pyrite surface, which play an important role in the molecular adsorption of glycine. While both chemical species (anion and zwitterion) adsorb on a sputtered pyrite surface, the anionic form of glycine is favoured. Nevertheless, in both treatments (sputtered or annealed surfaces), molecules evolve from zwitterionic to anionic species over time. Quantum mechanical calculations based in Density Functional Theory (DFT) suggest the energy required to generate vacancies increases with the number of vacancies produced, and the atomic charge of the Fe atoms that is next to a vacancy increases linearly with the number of vacancies. This leads to enhanced redox processes on the sputtered pyrite surface that favour the adsorption of glycine, which is confirmed experimentally by X-ray Photoemission Spectroscopy (XPS). We have investigated theoretically the efficiency of the adsorption process of the zwitterionic glycine onto vacancies sites: this reaction is exothermic, i.e. is energetically favoured and its energy increases with the number of defects, confirming the increased reactivity observed experimentally. The experiments show a treatment-dependent molecular selectivity of the pyrite surface.