Redox flow batteries (RFBs) are a promising solution to the increasing demand for energy storage as a transition from carbon-intensive to renewable energy sources continues. However, many flow battery chemistries still have low energy efficiencies due to their poorly understood overpotential contributions. To minimize RFB inefficiencies, many studies have explored oxidative treatment methods of their carbon-based electrodes which have provided conflicting results. Though three-electrode measurements are often the best method of isolating overpotential contributions, challenges associated with inserting a reference electrode into a typical laboratory flow battery design have limited most full cell studies to two-electrode measurements. Here, we demonstrate how a low-profile membrane-based reference electrode can be readily incorporated into standard laboratory full cell test systems. The reference electrode provides the ability to measure the potential of each electrode, providing new possibilities with full cell testing. This new membrane-based approach was used to examine overpotential contributions of a vanadium redox flow battery (VRFB) and a thermally regenerative flow battery (TRB). For the VRFB system, the negative electrode overpotential was consistently the largest contributor to cell overpotential. With untreated electrodes, the negative electrode added 227 mV of overpotential to the cell which was 95% of the total cell overpotential. After oxidative treatments, the negative electrode contribution decreased to 155 mV for the same setup. For the TRB system, the negative electrode was also the largest source of overpotential after ohmic contributions.