Abstract Heterostructures combining transition metal oxides, as compared to other materials, are able to accommodate very large amounts of epitaxial strain without breaking into islands or structural domains. Coherently strained interfaces are an interesting playground for the search of materials with enhanced ion diffusivities, of interest in devices for energy generation and storage. In this work we highlight the importance of the interface structure of highly strained YSZ/STO superlattices in determining an enhancement of their ionic conductivity. We show the role of growth orientation in controlling the structure and morphology of the interface. Results of density functional theory calculations are discussed, showing that the incompatibility of the oxygen positions at the interface planes plays a key role in stabilizing the high values of ionic conductivities.