A novel approach to incorporate cobalt atoms into a magnetite single crystal is demonstrated by a combination of x-ray spectro-microscopy, low-energy electron diffraction, and density-functional theory calculations. Co is deposited at room temperature on the reconstructed magnetite (001) surface filling first the subsurface octahedral vacancies and then occupying adatom sites on the surface. Progressive annealing treatments at temperatures up to 733 K diffuse the Co atoms into deeper crystal positions, mainly into octahedral ones with a marked inversion level. The oxidation state, coordination, and magnetic moments of the cobalt atoms are followed from their adsorption to their final incorporation into the bulk, mostly as octahedral Co(2+). This precise control of the near-surface Co atoms location opens up the way to accurately tune the surface physical and magnetic properties of mixed spinel oxides.