Single-crystals of TiO2 rutile were co-implanted with iron and cobalt to investigate the interplay between the role of these ions and their influence in the magnetic properties of the system. In the co-implanted crystals, both ions were implanted with the same nominal fluence, 5 × 1016 cm−2, and an implantation energy of 150 keV. The as-implanted single crystals exhibited superparamagnetic behaviour associated with the formation of nanosized aggregates. An annealing treatment at 1073 K induced recovery of the lattice structure and the appearance of a ferromagnetic phase. The evolution of the systems depends on the order of implantation of the two different ions.