The controlled self-assembly of polymer-stabilized quantum dots (QDs) into mesoscale aqueous spherical assemblies termed quantum dot compound micelles (QDCMs) using a two-phase gas-segmented microfluidic reactor is described. Self-assembly is initiated by the fast mixing of water (similar to 1 s) with a blend solution of polystyrene-coated QDs and amphiphilic polystyrene-block-poly(acrylic acid) stabilizing chains via chaotic advection within liquid plugs moving through a sinusoidal channel. Subsequent recirculating flow within a post-formation channel subjects the dynamic QDCMs to shear-induced processing, controlled via the flow rate and channel length, before a final quench into pure water. During processing, larger QDCMs within the initial population undergo breakup into smaller particles, resulting in smaller mean particle sizes, smaller relative standard deviations, and more skewed distribution shapes, as the overall shear exposure is increased. For these cases, shear-induced size reduction is sufficient to dominate surface tension-driven growth.