This in situ soft X-ray scanning microscopy electrochemical study of model proton exchange cathodic and anodic nano-fuel cells is exploring the evolving structure and chemical composition of key cell components represented by Au and Fe electrodes in contact with Nafion-ionic liquid composite electrolyte containing Pt black catalyst particles. Morphological and chemical changes of the electrodes as well as the chemical state and fate of the Fe species released into the electrolyte are monitored in short circuit and with applied cathodic or anodic polarization. The in situ X-ray absorption images of the cathodic cell fed with 2.5 × 10–5 mbar O2 have revealed corrosion-induced morphology changes in the Fe electrode, being more pronounced in the vicinity of Pt-black particles, and deposition of the Fe species released into the electrolyte, onto the intact Au counter electrode upon cathodic polarization. The Fe electrodes of the anodic cell containing NaBH4 in the electrolyte appear relatively more corrosion resistant. The Fe L3 absorption spectra taken in different locations within the Fe electrode have shown lateral variations in the relative ratio between Fe2+ and Fe3&4+ oxidation states, whereas the Fe species released into the RTIL electrolyte are only in the high Fe3&4+ oxidation states.