Ionomer membranes are employed in PEM fuel cells as the proton conducting element, but they also hold potential for catalytic applications in both hydrogen based and other low temperature fuel cells. In these applications the reactions of H2, CO, 02, H20 and other small molecules with metal-based catalysts are important to consider. Reactions of these species with perfluorocarbonsulfonic acid based ionomers (PFSA), of which Nafionsa are prototypical, containing Rh, Ru, Pt and other metal ions and particles are shown. Metal carbonyls form with metal ions that have been reduced in situ to reduced valence ions or to metal particles, by the combination of CO and H2O or with H2 directly. Metal nitrogen complexes also can be formed. In addition, the interactions of dissimilar metal ions leads to distinct species with NO or CO, for example, that are different from the products with either ion separately.