Continuous flow synthesis of semiconductor quantum dots (QDs) holds the promise of being highly reproducible, being scalable, and providing precise control of all reaction parameters. Here, we applied this technique to the aqueous synthesis of the Ag–In–S (AIS) core and AIS/ZnS core/shell QDs and optimized several parameters comprising reaction temperature, pressure, time, nature, and the ratio of precursors. Photoluminescence quantum yield (PLQY) values of 32%/44% (average/best) for the core and 77%/83% for the core/shell system have been obtained in short reaction times (8–15 min). We demonstrate by means of combined structural and optical studies that the high PLQY originates from donor–acceptor pair recombination processes, involving essentially [In$_{Ag}$$^{2+}$ + 2V$_{Ag}$$^–$] defect complexes whose formation is favored by the large excess of indium used (In:Ag ratio of 4:1), and the low reaction temperature (100–120 °C). The structural disorder is further enhanced during ZnS shell growth, which in addition to surface passivation and removal of nonradiative decay channels leads to the partial diffusion of the added zinc ions into the AIS core and the formation of ZnIn− antisite defects. The presented method provides excellent reproducibility and high scalability, facilitating the large-scale production of highly luminescent AIS/ZnS QDs.