Phosphoric acid is amphoteric and has been used to dope basic polymer, e.g. polybenzimidazole, membranes and acidic polymer, e.g. perfluorosulfonic acid, membranes. Both membrane systems exhibit high proton conductivities at temperatures above 100 °C under anhydrous conditions. The former has been developed into a commercial fuel cell technology while the latter can only deliver a few mA cm−2 in fuel cells and hydrogen pumping cells. In this work, it is experimentally verified that the current window of acid doped perfluorosulfonic acid membranes in electrochemical cells under dry conditions is limited by the migration of H4PO4 + species in combination with the slow H3PO4 diffusion. The phosphoric acid dynamics were monitored in a cell equipped with integrated reference electrodes in the electrolyte membrane, which allowed for quantification of the phosphoric acid in different membrane segments. From the time-resolved measurements, the H4PO4 + transference number was found to be as high as 52% under dry conditions. In combination with the slow H3PO4 back-diffusion, which was 5–6 orders of magnitude lower than that of water, the migration of H4PO4 + towards the cathode results in rapid resistance increase at the anode-membrane interface, ultimately leading to the cell failure.