We report here on the magnetic coupling taking place between Fe3O4 and Co layers across an organic monolayer of α-sexithiophene (6T). The controlled growth of 6T ultrathin films on epitaxial Fe3O4 surfaces allows to prepare highly homogeneous insulating layers with thicknesses in the range 0.5–2.0 monolayers (ML). A combined study using vibrating sample magnetometry and polarized neutron reflectivity reveals that hybrid Fe3O4/6T/Co tunnel junctions show different magnetic couplings depending on the 6T thickness. In particular, magnetic coupling between Fe3O4 and Co layers separated by 1 ML of 6T is consistent with anti-ferromagnetic coupling, opening new perspectives for controlling magnetization in organic spintronic devices.