Colloidal quantum dots (QDs) offer dramatic potential due to their size-dependent optical properties. Lack of facile synthesis methods for precise and reproducible size and composition, however, presents an extant barrier to their widespread use. Here, we report the use of droplet microfluidics for the simple and highly reproducible synthesis of cadmium sulfide (CdS) and cadmium selenide (CdSe) QDs without the use of harsh solvents and in ambient conditions. Our approach uses a liquid-liquid barrier between two immiscible liquids to generate a digital droplet reactor. This reaction droplet is easily controlled and manipulated and offers enhanced mixing when coupled to a helical mixer, resulting in a significant reduction in size distribution compared to benchtop procedures. Furthermore, QD characteristics have been modeled and predicted based on the parameters of the microfluidic device. We believe this method overcomes the current manufacturing challenges with synthesizing nanostructures, which is required for the next generation of nanosensors.