Engineered peptide ligands with exceptionally high affinity for metal can self-assemble with nanoparticles in biological fluids. A high-affinity dendrimeric peptide ligand for CdSe-ZnS quantum dots (QDs) exhibited very fast association kinetics with QDs and reached equilibrium within 2 s. Here, we have combined a droplet-based microfluidic device with fluorescence detection based on Förster resonance energy transfer (FRET) to provide subsecond resolution in dissecting this fast self-assembly kinetics in solution. This work represents the first application of microfluidic devices to ligand-particle assembly for the measurement of fast assembly kinetics in solution.