X-ray photoelectron spectroscopy (XPS) is one of the most common techniques used to analyze the surface composition of catalysts and support materials used in polymer electrolyte membrane (PEM) fuel cells and electrolyzers, providing important insights for further improvement of their properties. Characterization of catalyst layers (CLs) is more challenging, which can be at least partially attributed to the instability of ionomer materials such as Nafion during measurements. This work explores the stability of Nafion during XPS measurements, illuminating and addressing Nafion degradation concerns. The extent of Nafion damage as a function of XPS instrumentation, measurement conditions, and sample properties was evaluated across multiple instruments. Results revealed that significant Nafion damage to the ion-conducting sulfonic acid species (>50% loss in sulfur signal) may occur in a relatively short time frame (tens of minutes) depending on the exact nature of the sample and XPS instrument. This motivated the development and validation of a multipoint XPS data acquisition protocol that minimizes Nafion damage, resulting in reliable data acquisition by avoiding significant artifacts from Nafion instability. The developed protocol was then used to analyze both thin film ionomer samples and Pt/C-based CLs. Comparison of PEM fuel cell CLs to Nafion thin films revealed several changes in Nafion spectral features attributed to charge transfer due to interaction with conductive catalyst and support species. This study provides a method to reliably characterize ionomer-containing samples, facilitating fundamental studies of the catalyst-ionomer interface and more applied investigations of structure-processing-performance correlations in PEM fuel cell and electrolyzer CLs.