AbstractSelf‐diffusion is a fundamental physical process that, in solid materials, is intimately correlated with both microstructure and functional properties. Local transport behavior is critical to the performance of functional ionic materials for energy generation and storage, and drives fundamental oxidation, corrosion, and segregation phenomena in materials science, geosciences, and nuclear science. Here, an adaptable approach is presented to precisely characterize self‐diffusion in solids by isotopically enriching component elements at specific locations within an epitaxial film stack, and measuring their redistribution at high spatial resolution in 3D with atom probe tomography. Nanoscale anion diffusivity is quantified in a‐Fe₂O₃ thin films deposited by molecular beam epitaxy with a thin (10 nm) buried tracer layer highly enriched in ¹⁸O. The isotopic sensitivity of the atom probe allows precise measurement of the initial sharp layer interfaces and subsequent redistribution of ¹⁸O after annealing. Short‐circuit anion diffusion through 1D and 2D structural defects in Fe₂O₃ is also directly visualized in 3D. This versatile approach to study precisely tailored thin film samples at high spatial and mass fidelity will facilitate a deeper understanding of atomic‐scale diffusion phenomena.