Abstract: The possibility to control oxygen transport in one of the most promising solid oxide fuel cell cathode materials, La0.6Sr0.4CoO3−δ, by controlling lattice strain raises questions regarding the contribution of atomic scale effects. Here, high-resolution transmission electron microscopy revealed the different atomic structures in La0.6Sr0.4CoO3−δ thin films grown under tensile and compressive strain conditions. The atomic structure of the tensile-strained film indicated significant local concentration of the oxygen vacancies, with the average value of the oxygen non-stoichiometry being much larger than for the compressive-strained film. In addition to the vacancy concentration differences that are measured by isotope exchange depth profiling, significant vacancy ordering was found in tensile-strained films. This understanding might be useful for tuning the atomic structure of La0.6Sr0.4CoO3−δ thin films to optimize cathode performance.