Supported single atoms provide an opportunity to design new heterogeneous catalysts while optimizing the utilization of noble metals. However, identification of the active single-atom structure is required for understanding the reaction mechanism and guiding catalyst design. Here, we use in situ infrared spectroscopy, operando X-ray absorption spectroscopy and quantum chemical calculations to identify the active single-atom complex as well as the resting state of the Ir/MgAl2O4 catalysts during the low-temperature CO oxidation. In contrast to poisoning of iridium nanoparticles by CO, here we show that the formation of Ir(CO) on single atoms results in a different reaction mechanism and high activity for low-temperature CO oxidation. This is due to the ability of single atoms to coordinate with multiple ligands, where Ir(CO) provides an interfacial site for facile O2 activation between Ir and Al and lowers the reaction barrier between gas-phase CO(g) and *O in Ir(CO)(O) through an Eley–Rideal mechanism.