Low temperature radioluminescence and thermoluminescence spectra of ZnO track numerous changes produced by copper ion implantation into the surface layer. A significant, but unexpected, feature is that the bulk crystal becomes modified by the stress generated in the surface layer. This is reflected by the energy of intrinsic band gap emission. There are also differences in the spectra and peak temperatures of the thermoluminescence components, consistent with such a structural relaxation. The copper implant layer is both absorbing and reflective, so this introduces major distortions on the radioluminescence component from the bulk region, since the bulk luminescence signals are transmitted through, or reflected from, the implant layer. The temperature dependence of the spectra includes anomalies that are typical of changes driven by phase transitions of nanoparticle inclusions. Overall, the features of bulk relaxation, spectral distortion, and detection of nanoparticle inclusions are rarely considered for ion implanted luminescence studies, but the data suggest they are almost inevitable in a wide range of implanted materials.