Nanoscale materials modified by crystal defects exhibit significantly different behaviours upon chemical reactions such as oxidation, catalysis, lithiation and epitaxial growth. However, unveiling the exact defect-controlled reaction dynamics (e.g. oxidation) at atomic scale remains a challenge for applications. Here, using in situ high-resolution transmission electron microscopy and first-principles calculations, we reveal the dynamics of a general site-selective oxidation behaviour in nanotwinned silver and palladium driven by individual stacking-faults and twin boundaries. The coherent planar defects crossing the surface exhibit the highest oxygen binding energies, leading to preferential nucleation of oxides at these intersections. Planar-fault mediated diffusion of oxygen atoms is shown to catalyse subsequent layer-by-layer inward oxide growth via atomic steps migrating on the oxide-metal interface. These findings provide an atomistic visualization of the complex reaction dynamics controlled by planar defects in metallic nanostructures, which could enable the modification of physiochemical performances in nanomaterials through defect engineering.