Properties of complex oxide thin films can be tuned over a range of values as a function of mismatch, composition, orientation, and structure. Here, we report a strategy for growing structured epitaxial thermoelectric thin films leading to improved Seebeck coefficient. Instead of using single-crystal sapphire substrates to support epitaxial growth, Ca3Co4O9 films are deposited, using the Pulsed Laser Deposition technique, onto Al2O3 polycrystalline substrates textured by spark plasma sintering. The structural quality of the 2000 Å thin film was investigated by transmission electron microscopy, while the crystallographic orientation of the grains and the epitaxial relationships were determined by electron backscatter diffraction. The use of a polycrystalline ceramic template leads to structured films that are in good local epitaxial registry. The Seebeck coefficient is about 170 μV/K at 300 K, a typical value of misfit material with low carrier density. This high-throughput process, called combinatorial substrate epitaxy, appears to facilitate the rational tuning of functional oxide films, opening a route to the epitaxial synthesis of high quality complex oxides.