In this study, a detailed structural characterization of epitaxial La0.6Sr0.4CoO3−δ (LSC) films grown in (100), (110), and (111) orientations was conducted. LSC is a model air electrode material in solid oxide fuel and electrolysis cells and understanding the correlation of bulk structure and catalytic activity is essential for the design of future electrode materials. Thin films were grown on single crystals of the perovskite material La0.95Sr0.05Ga0.95Mg0.05O3−δ cut in three different directions. This enabled an examination of structural details at the atomic scale for a realistic material combination in solid oxide cells. The investigation involved the application of atomic force microscopy, X-ray diffraction, and high-resolution transmission electron microscopy to explore the distinct properties of these thin films. Interestingly, ordering phenomena in both cationic as well as anionic sublattices were found, despite the fact that the thin films were never at higher temperatures than 600 °C. Cationic ordering was found in spherical precipitates, whereas the ordering of oxygen vacancies led to the partial transition to brownmillerite in all three orientations. Our results indicate a very high oxygen vacancy concentration in all three thin films. Lattice strains in-plane and out-of-plane was measured, and its implications for the structural modifications are discussed.