The controlled self-assembly of polymer-stabilized quantum dots (QDs) into mesoscale aqueous spherical assemblies using microfluidics is described. In a flow-focusing configuration, self-assembly is initiated by the addition of water to a blended solution of polystyrene-coated QDs and amphiphilic polystyrene-block-poly(acrylic acid) stabilizing chains and terminated in a downstream quench step. The on-chip evolution of assemblies is monitored through fluorescence microscopy, and particle size distributions are determined off-chip by transmission electron microscopy. On-chip size control of the assemblies is demonstrated via both the average water concentration in the channel and the flow rate.