In this talk, I will show that thin-film deposition by molecular beam epitaxy (MBE) allows ultrahigh purity materials of this kind to be synthesized, together with accurate control over their thickness, doping level, and strain state for predictable structural and property modifications. In combination with advanced transmission electron microscopy (TEM), secondary ion mass spectrometry (SIMS), and theoretical modeling, we were able to characterize and simulate ion transport and phase transition processes at a comparable length scale to provide fundamental insight into these processes. In one example, we show that ordered oxygen vacancy planes in SrCrO3-δ under different strain states (compressive vs. tensile) displays drastically different phase stability and O2- ion transport properties, which is of considerable interest in solid oxide fuel cells where fast oxygen ion transport at lower operating temperature is highly desired. In another example, I will present how we tune the structure and electronic properties of WO3 epitaxial thin films, and use them as model cathode materials for in situ TEM studies. The atomic scale ion (Li+, Na+, and Ca2+) intercalation, accompanied with a monoclinic to cubic phase transition, together with subsequent conversion reactions are revealed by STEM, EELS, NBD, and theory.