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Anion exchange membrane fuel cells (AEMFC) are potentially very low-cost replacements for proton exchange membrane fuel cells. However, AEMFCs suffer from one very serious drawback: significant performance loss when CO2 is present in the reacting oxidant gas (e.g., air) due to carbonation. Although the chemical mechanisms for how carbonation leads to voltage loss in operating AEMFCs are known, the way those mechanisms are affected by the properties of the anion exchange membrane (AEM) has not been elucidated. Therefore, this work studies AEMFC carbonation using numerous high-functioning AEMs from the literature and it was found that the ionic conductivity of the AEM plays the most critical role in the CO2-related voltage loss from carbonation, with the degree of AEM crystallinity playing a minor role. In short, higher conductivity—resulting either from a reduction in the membrane thickness or a change in the polymer chemistry—results in faster CO2 migration and emission from the anode side. Although this does lead to a lower overall degree of carbonation in the polymer, it also increases CO2-related voltage loss. Additionally, an operando neutron imaging cell is used to show that as AEMFCs become increasingly carbonated their water content is reduced, which further drives down cell performance.