There is a critical need for higher performing proton exchange membranes for electrochemical energy conversion devices that would enable higher temperature and drier operating conditions to be utilized. A novel approach is to utilize multiacid side chains in a perfluorinated polymer, maintaining the mechanical properties of the material, while dramatically increasing the ion-exchange capacity; however, as we show in this paper, the more complex side chain gives rise to unexpected physical phenomena in the material. We have thoroughly investigated a doubly functionalized perfluorosulfonic imide acid side chain perfluorinated polymer (PFIA), the simplest of many possible multiacid side chains currently being developed. The material is compared to its simpler perfluorosulfonic acid (PFSA) analogue via a battery of characterization and modeling investigations. The doubly functional side chain profoundly influences the properties of the PFIA polymer as it gives rise to both inter- and intraside chain interactions. These affect the nature of thermal decomposition of the material but, more importantly, force the backbone of the polymer into an unusually highly ordered more crystalline configuration. Under water saturated conditions, the PFIA has the same proton conductivity as the PFSA material, indicating that the additional proton does not contribute to the ionic conductivity, but the PFIA shows higher proton conductivity at lower RH conditions owing to dynamic changes in its local molecular environment. A transition is observed between 30 and 60 °C, indicating an order/disorder transition that is not present in the PFSA analogue. The mechanism of proton transport in the PFIA is due to more delocalized protons and more flexible side chains with better-dispersed, smaller water clusters forming the hydrophilic domains than in the PFSA analogue.