Inputs of nitrogen into terrestrial ecosystems, mainly via the use of ammonium-based fertilizers in agroecosystems, are enormous, but its fate under elevated atmospheric carbon dioxide (CO₂) is not well understood. We have taken advantage of a 15-year free air CO₂ enrichment study to investigate the influence of elevated CO₂ on the transformation of ammonium-nitrogen in a rice ecosystem in which ammonium is usually assumed to be stable under anaerobic conditions. We demonstrate that elevated CO₂ causes substantial losses of ammonium-nitrogen that result from anaerobic oxidation of ammonium coupled to reduction of iron. We identify a new, autotrophic member of the bacterial order Burkholderiales that may use soil CO₂ as a carbon source to couple anaerobic ammonium oxidation and iron reduction. These findings offer insight into the coupled cycles of nitrogen and iron in terrestrial ecosystems and raise questions about the loss of ammonium-nitrogen from arable soils under future climate-change scenarios.