Layered cobaltite Ca3Co4O9 is one of the most interesting materials for energy conversion due to its excellent thermoelectric properties and stability at high temperatures. However, the best performance of this material is achieved for single crystals and epitaxial films. Within this framework, an important role is played by the substrate, which should promote epitaxial growth and that should have suitable thermal properties for its integration in devices. In this work, we report on the preparation of epitaxial thin films of Ca3Co4O9 by sputtering using low cost ceramic target on cubic yttria-stabilized zirconia (YSZ(100)) that is typically the standard for low thermal conductivity material and on hexagonal sapphire (Al2O3(0001)). The quality of the epitaxial films and its microstructure has been studied to explain the thermoelectric properties obtained for both substrates. YSZ(100) substrate provides Ca3Co4O9 films with enhanced Seebeck coefficient and Al2O3(0001) allows improved conductive Ca3Co4O9 films that finally, at 200 degrees C, results in a substrate-modified Z'T figure of merit one order of magnitude higher for Ca3Co4O9 on YSZ(100) than on Al2O3(0001) substrate. (C) 2017 Elsevier B.V. All rights reserved.