Single‐atom catalysts (SACs) bridge homo‐ and heterogeneous catalysis because the active site is a metal atom coordinated to surface ligands. The local binding environment of the atom should thus strongly influence how reactants adsorb. Now, atomically resolved scanning‐probe microscopy, X‐ray photoelectron spectroscopy, temperature‐programmed desorption, and DFT are used to study how CO binds at different Ir1 sites on a precisely defined Fe3O4(001) support. The two‐ and five‐fold‐coordinated Ir adatoms bind CO more strongly than metallic Ir, and adopt structures consistent with square‐planar IrI and octahedral IrIII complexes, respectively. Ir incorporates into the subsurface already at 450 K, becoming inactive for adsorption. Above 900 K, the Ir adatoms agglomerate to form nanoparticles encapsulated by iron oxide. These results demonstrate the link between SAC systems and coordination complexes, and that incorporation into the support is an important deactivation mechanism.