The study of flow batteries (FBs) requires the development of tools able to evaluate their performance during operation in a reliable and simple way. In this work, we present an experimental set-up that allows the on-line monitoring of the half-cells state of charge and apparent overpotentials on the positive and negative electrodes during battery operation. These measurements are feasible by using additional flow cells that include a reference electrode on each side. We used the experimental set-up to study the performance of the vanadium system as well as a previously reported stable organic couple. The studies consisted on short cycling operation at different current densities and polarization curves at different flow rates and states of charge. By confirming previous results obtained for vanadium-FBs and extending the analysis to further systems, we demonstrated that this approach provides a reliable deeper insight into the battery performance and the processes taking place during operation.