Polymer electrolytes such as perfluorosulfonic acid (PFSA) are key to a variety of electrochemical and clean energy applications. Many analytical techniques for characterizing nanostructured devices containing polymer electrolytes use high-energy electrons or X-rays, which can severely damage soft matter. To better analyze these materials, it is important to understand the chemical, physical, and spectroscopic changes that occur due to radiation damage. Soft X-ray damage to PFSA was characterized using a combination of X-ray microscopy, X-ray absorption spectroscopy, infrared spectroscopy, fluorescence imaging, and atomic force microscopy. X-ray exposure induces substantial and selective loss of fluorine, preferential cleavage of the side chains, and physical ablation of the polymer. The combination of multiple imaging and spectroscopy modalities provides detailed insight into radiation damage mechanisms.