We intend to develop an in situ near-infrared spectroscopic solution for monitoring the nutrient composition (e.g., lactate concentration) in microfluidic channels of organ-on-chip devices. In this work, the effects of the geometry, surface quality, and architecture of the micro-volume cuvettes were characterized and optimized considering the signal-to-noise ratio and sensitivity of the proposed spectroscopic method in case of aqueous solutions. The applicability of the micro-volume near-infrared spectroscopy method using this specially designed microfluidic cuvette was proven.