This work reports on the local structure of as-implanted and thermally-treated single Co:ZnO nanowires studied using a hard X-ray nanoprobe. Although the Co ions are incorporated into the wurtzite ZnO lattice, X-ray absorption near edge structure data show high structural disorder in the as-implanted nanowires compared with the annealed ones. In particular, extended X-ray absorption fine structure from single wires reveals a lattice distortion around Zn sites of the as-implanted nanowires, which involves an expansion of the stable wurtzite lattice. The observed local lattice response confirms good recovery of the implantation-induced damage within the ZnO lattice through a thermal treatment.