The applicability of analyzing by Mößbauer spectroscopy the structural changes of Fe–N–C catalysts that have been tested at the cathode of membrane electrode assemblies in proton exchange membrane (PEM) fuel cells is demonstrated. The Mößbauer characterization of powders of the same catalysts was recently described in our previous publication. A possible change of the iron species upon testing in fuel cell was investigated here by Mößbauer spectroscopy, energy-dispersive X-ray cross-sectional imaging, and neutron activation analysis. Our results show that the absorption probability of γ rays by the iron nuclei in Fe–N–C is strongly affected by the presence of Nafion and water content. A detailed investigation of the effect of an oxidizing treatment (1.2 V) of the non-noble cathode in PEM fuel cell indicates that the observed activity decay is mainly attributable to carbon oxidation causing a leaching of active iron sites hosted in the carbon matrix.