Proton exchange membrane (PEM) electrolysis is considered a promising technique for producing green hydrogen at high purity, yet it has not been implemented industrially on a large scale. To make this technology economically feasible, the industry is in search of ways to recycle the membranes and the catalyst material. A particular benefit of membrane recycling is that it can prevent high financial penalties, as a ban on the production of PFAS materials is currently under discussion. One suggested recycling process is based on the use of alcohol to separate the catalyst material from the PEM. However, the influence of the separation mechanism on the structure of the PEM is often disregarded. In this work, ¹⁹ F solid-state NMR techniques as well as ¹H diffusion NMR were applied to analyse the invasiveness of such a separation technique on a short-side chain perfluorosulfonic acid (ssc- PFSA) ionomer, which is a widely used PEM material for high-durability electrolysis cells. Therefore, a sample preparation routine was established to mimic relevant states in the conditioning and recycling process of PEM materials. Based on the evolution of ¹⁹F spectra, it was found that a water-isopropanol mixture causes changes in the chemical composition of the polymer structure. In conjunction with signal analysis, various degradation pathways are discussed that are initiated by ultrasound during electrode separation. Relaxation experiments also suggest that the polymer morphology is significantly altered during the entire production process, and particularly during the separation process.