Perfluorosulfonic acid ionomers (PFSAs) are the benchmark materials used as proton exchange membranes in fuel cells due to their exceptional proton conductivity and chemical and mechanical stability. Typical PFSAs consist of a PTFE backbone with perfluoroether sidechains bearing pendant sulfonic acid groups. PFSAs of different ion contents and sidechain compositions have been developed in an effort to optimize functionality while maintaining mechanical stability. One such ionomer is 3M’s perfluoroimide acid (PFIA) containing a sulfonimide acid group in addition to the sulfonic acid on each sidechain to increase proton conductivity while preserving TFE backbone segments to maintain sufficient crystallinity. In this study, we investigate the effect of this additional acidic site on the thermomechanical properties and morphology of PFIA compared to the single acid PFSA. Utilizing alkylammonium counterions we are able to systematically manipulate the strength of the physically crosslinked network in the perfluorinated ionomers to probe the origins of thermomechanical transitions. The addition of the sulfonimide in PFIA leads to interesting differences in the morphology and thermomechanical properties including the appearance of an anomalous glass transition that is not observed in single acid PFSAs. Techniques including dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), and variable temperature small angle x-ray scattering (SAXS) are utilized to probe the anomalous glass transition and assign it to the true glass transition temperature for PFIA.