The mechanism of carbon monoxide oxidation over gold was explored using a model planar catalyst consisting of monodisperse gold nanoparticles periodically arranged on a single crystal SiO2/Si(111) substrates using a combination of Grazing Incidence Small Angle X-ray Scattering and Grazing Incidence X-ray Diffraction (GISAXS/GIXD) under reaction conditions. It is shown that nanoparticle composition, size and shape change when the catalyst is exposed to reactive gases. During CO oxidation, the particle’s submergence depth with respect to the surface decreases due to the removal of gold oxide at the metal-support edge, meanwhile the particle ‘flattens’ to maximise the number of the reaction sites along its perimeter. The effect of the CO concentration on the catalyst structure is also discussed. Our results support the dual catalytic sites mechanism whereby CO is activated on the gold surface whereas molecular oxygen is dissociating at the gold-support interface.