GaN nanowires (NWs) were implanted with low fluences of rare-earth ions. Ion channelling measurements revealed the perfect vertical alignment of the NWs and their orientation with respect to the silicon substrate. The channelling properties were not altered by the implantation or annealing treatments, and X-ray diffraction measurements demonstrated the full structural recovery of the NWs after post-implant annealing. Strong Pr-related cathodoluminescence at room temperature was observed after annealing and results indicate the successful incorporation of Pr on substitutional Ga sites inside the NWs. Furthermore, an intriguing behaviour of the cathodoluminescence as a function of the electron beam irradiation time was observed, suggesting that Pr luminescence can be sensitized by the same defect that is responsible for the yellow luminescence band frequently seen in GaN. The formation of this Pr–defect complex can be controlled by defect engineering using a combination of ion implantation, annealing and electron beam irradiation, and leads to an increase of the Pr luminescence by a factor of more than 4.