Ultralow energy (ULE) ion implantation is being increasingly applied to the modification of 2D materials, in particular, for substitutional doping and intercalation of graphene. Implantation-induced defects, whether desired or not, have a strong impact on the properties of graphene. Significant research has been devoted to vacancy-related defects however, disorder induced by ion irradiation in the ULE limit, that is, for energies below the vacancy-formation threshold, remains poorly understood. Here, we focus on that regime and report the formation of defects resulting from the breaking of C–C sp2 bonds and formation of C-substrate bonds. As a model system we used epitaxial graphene grown on Cu(111) and on Pt(111), subsequently implanted with He, Ne and Ar at energies between 15 eV and 40 eV. The bond defect density is found to increase with increasing energy and atomic number of the implanted element. These findings significantly advance our understanding of disorder induced in graphene by ULE ion implantation, while simultaneously revealing the potential for exploiting such bond defects for physical or chemical functionalization. In particular, these bond defects can be generated with a high degree of selectivity since they occur in the low-energy limit (at least down to 15 eV), significantly below the energies required to form stable vacancies.