3-Aminopropyltrimethoxysilane (APTMS) was used as ligand to prepare ZnO@APTMS, Cu2+-doped ZnO (ZnO:Cu@APTMS) and ZnO quantum dots (QDs) with chemisorbed Cu2+ ions at their surface (ZnO@APTMS/Cu). The dots have a diameter of ca. 5 nm and their crystalline and phase purities and composition were established by X-ray diffraction, transmission electron microscopy, UV-visible and fluorescence spectroscopies and by X-ray photoelectron spectroscopy. The effect of Cu2+ location on the ability of the QDs to generate reactive oxygen species (ROS) under light irradiation was investigated. Results obtained demonstrate that all dots are able to produce ROS (•OH, O2•−, H2O2 and 1O2) and that ZnO@APTMS/Cu QDs generate more •OH and O2•− radicals and H2O2 than ZnO@APTMS and ZnO:Cu@APTMS QDs probably via mechanisms associating photo-induced charge carriers and Fenton reactions. In cytotoxicity experiments conducted in the dark or under light exposure, ZnO@APTMS/Cu QDs appeared slightly more deleterious to Escherichia coli cells than the two other QDs, therefore pointing out the importance of the presence of Cu2+ ions at the periphery of the nanocrystals. On the other hand, with the lack of photo-induced toxicity, it can be inferred that ROS production cannot explain the cytotoxicity associated to the QDs. Our study demonstrates that both the production of ROS from ZnO QDs and their toxicity may be enhanced by chemisorbed Cu2+ ions, which could be useful for medical or photocatalytic applications.