Within the emerging field of proton-conducting fuel cells, BaZr0.9Y0.1O3-δ (BZY10) is an attractive material due to its high conductivity and stability. The fundamentals of conduction in sintered pellets and thin films heterostructures have been explored in several studies; however, the role of crystallographic orientation, grains, and grain boundaries is poorly understood for proton conduction. This article reports proton conduction in a self-assembled multi-oriented BZY10 thin film grown on top of a (110) NdGaO3 substrate. The multiple orientations are composed of different lattices, which provide a platform to study the lattice-dependent conductivity through different orientations in the vicinity of grain boundary between them and the substrate. The crystalline stacking of each orientation is confirmed by X-ray diffraction analysis and scanning transmission electron microscopy. The transport measurements are carried out under different gas atmospheres. The highest conductivity of 3.08 × 10-3 S cm-1 at 400 °C is found under a wet H2 environment together with an increased lattice parameter of 4.208 Å, while under O2 and Ar environments, the film shows lower conductivity and lattice parameter. Our findings not only demonstrate the role of crystal lattice for conduction properties but also illustrate the importance of self-assembled strategies to achieve high proton conduction in BZY10 thin films.