The origin of photoluminescence in copper indium sulfide (CIS) quantum dots (Qdots) has previously been ascribed to a donor-acceptor pair (DAP) recombination, with a crystal lattice defect implicated as the origin of the donor state. In this study, electron energy-loss spectroscopy (EELS) was used to observe defect-rich compositional domains within individual CIS Qdots, supporting a model of defect-state-mediated photoluminescence for these particles, and identifying them as an ideal model system for future study of lattice defects on Qdot properties.