A key question in materials science is how fast properties evolve, which relates to the kinetics of phase transformations. In metals, kinetics is primarily connected to diffusion, which for substitutional elements is enabled via mobile atomic-lattice vacancies. In fact, non-equilibrium vacancies are often required for structural changes. Rapid quenching of various important alloys, such as Al- or Mg-alloys, results for example in natural aging, i.e. slight movements of solute atoms in the material, which significantly alter the material properties. In this study we demonstrate a size effect of natural aging in an AlMgSi alloy via atom probe tomography with near-atomic image resolution. We show that non-equilibrium vacancy diffusional processes are generally stopped when the sample size reaches the nanometer scale. This precludes clustering and natural aging in samples below a certain size and has implications towards the study of non-equilibrium diffusion and microstructural changes via microscopy techniques.