Due to the high conductivity and stability, perfluorinated sulfonic acid (PFSA) proton exchange membranes such as Nafion are currently the standard for polymer electrolyte membranes (PEMs). While boasting superior conductive properties at standard conditions, Nafion dehydrates at high temperature and low humidity, drastically compromising its performance. While functionalization of PFSA membranes with phosphoric acid has been shown to improve conductivity under low-humidity conditions, these membranes still require optimization as they lack a practical level of conductivity. In this study, we use computational methods to investigate the nanophase-segregation and transport in phosphoric acid membranes in comparison to Nafion membranes, and analyze the effect of side chain length on these two properties. It is found that, as in sulfonic acid membranes, larger water clusters are formed in phosphoric acid membranes with longer side chains. However, unlike in sulfonic acid membranes, the phosphoric acid groups associate closely with one another via hydronium bridging, which suppresses proton hopping. Therefore, it is inferred that the proton transport is decreased with increasing the phosphoric acid side chain length. Based on these results, we recommend opting for shorter side chain lengths when designing phosphoric acid membranes.