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Abstract Despite the ubiquitous presence of passivation on most metal surfaces, the microscopic‐level picture of how surface passivation occurs has been hitherto unclear. Using the canonical example of the surface passivation of aluminum, here in situ atomistic transmission electron microscopy observations and computational modeling are employed to disentangle entangled microscopic processes and identify the atomic processes leading to the surface passivation. Based on atomic‐scale observations of the layer‐by‐layer expansion of the metal lattice and its subsequent transformation into the amorphous oxide, it is shown that the surface passivation occurs via a two‐stage oxidation process, in which the first stage is dominated by intralayer atomic shuffling whereas the second stage is governed by interlayer atomic disordering upon the progressive oxygen uptake. The first stage can be bypassed by increasing surface defects to promote the interlayer atomic migration that results in direct amorphization of multiple atomic layers of the metal lattice. The identified two‐stage reaction mechanism and the effect of surface defects in promoting interlayer atomic shuffling can find broader applicability in utilizing surface defects to tune the mass transport and passivation kinetics, as well as the composition, structure, and transport properties of the passivation films.