Antibiotic resistance is an imminent threat to human health, requiring the development of effective alternate antibacterial agents. One such alternative includes nanoparticle (photo)catalysts that are good at producing reactive oxygen species (ROS). Herein, we report the design and preparation of nitrogen-doped carbon dots functionalized with atomically dispersed copper centers by Cu-N coordination (Cu/NCD) that exhibit apparent antibacterial activity toward Gram-negative Escherichia coli (E. coli) under photoirradiation. The growth of E. coli cells is found to be markedly inhibited by Cu/NCD under 365 nm photoirradiation, whereas no apparent inhibition is observed in the dark or with the copper-free carbon dots alone. This is ascribed to the prolonged photoluminescence lifetime of Cu/NCD that facilitates the separation of photogenerated electron-hole pairs and ROS formation. The addition of tert-butyl alcohol is found to completely diminish the antimicrobial activity, suggesting that hydroxyl radicals are responsible for microbial death. Consistent results are obtained from fluorescence microscopic studies using CellROX green as the probe. Similar bactericidal behaviors are observed with Gram-positive Staphylococcus epidermidis (S. epidermidis). The copper content within the carbon material is optimized at a low loading of 1.09 wt %, reducing the possibility of toxic copper-ion leaching. Results from this study highlight the significance of carbon-based nanocomposites with isolated metal species as potent antimicrobial reagents.