Current combinatorial chemistry technology often utilizes well plates in with individual volumes on the order of a microliter. When screening for suitable targets that bind with a certain protein, yet the protein is only available in small quantities and/or very expensive, many more different potential targets can be screened with the same amount of protein if the volume of each reaction well is smaller. Downscaling of present well plate technology, however, is hampered by several issues: rapid dry out of each well due to evaporation of the solvent, challenges in being able to detect a hit, and the need for more advanced and thus more costly fluid handling robots. We present a microfluidic well plate chip with reactor volumes on the order of 0.2 nL. This chip is integrated with a photonic crystal biosensor, which can determine differences in binding affinities of molecules with an immobilized protein target on the sensor surface via changes in optical response. The performance of the microfluidic chip was demonstrated by sample bulk refractive index sensitivity experiments and protein binding experiments.