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Interface-dominated materials such as nanocrystalline thin films have emerged as an enthralling class of materials able to engineer functional properties of transition metal oxides widely used in energy and information technologies. In particular, it has been proved that strain-induced defects in grain boundaries of manganites deeply impact their functional properties by boosting their oxygen mass transport while abating their electronic and magnetic order. In this work, the origin of these dramatic changes is correlated for the first time with strong modifications of the anionic and cationic composition in the vicinity of strained grain boundary regions. We are also able to alter the grain boundary composition by tuning the overall cationic content in the films, which represents a new and powerful tool, beyond the classical space charge layer effect, for engineering electronic and mass transport properties of metal oxide thin films useful for a collection of relevant solid state devices.