High performance semiconducting thin films enable the implementation of thermoelectric generators as energy harvesters for wearable applications. The optimization of material properties is critical in such applications, as restrictions introduced by the substrates on deposition temperature and active layer size, impose fundamental limitations on performance. Here we present the optimization of sputtered bismuth telluride, BiTe, and germanium telluride, GeTe, annealed at 300 °C allowing comfortable development on polyimide substrates. The crystal structure and material composition of the films, before and after annealing, were measured by X-ray diffraction and X-ray photoelectron spectroscopy to reveal the changes in the material that enhanced the performance. The power factor of the BiTe films increased post-anneal up to 2.2 µW/cmK2, whilst the GeTe increased over 5 orders of magnitude to 7.6 µW/cmK2. A flexible thermoelectric generator was fabricated with pairs of alternating annealed BiTe and GeTe strips, reaching 7 nW per pair of output power at a temperature difference of 20 °C. Using this micro-fabrication process of thin films, compatible to roll-to-roll technologies, the physical dimensions of the generators can be tuned to deliver the required power, for providing storage energy for on-demand devices such as periodic sensing.