Hybrid thermoelectric flexible films based on poly(3,4-ethylenedioxythiophene) (PEDOT) nanoparticles and carbon nanotubes were prepared by using layer-by-layer (LbL) assembly. The employed PEDOT nanoparticles were synthesized by oxidative miniemulsion polymerization by using iron(III) p-toluenesulfonate hexahydrate (FeTos) as an oxidant and poly(diallyldimethylammonium chloride) (PDADMAC) as stabilizer. Sodium deoxycholate (DOC) was used as a stabilizer to prepare the aqueous dispersions of the carbon nanotubes. Hybrid thermoelectric films were finally prepared with different monomer/oxidant molar ratios and different types of carbon nanotubes, aiming to maximize the power factor (PF). The use of single-wall (SWCNT), double-wall (DWCNT), and multiwall (MWCNT) carbon nanotubes was compared. The Seebeck coefficient was measured by applying a temperature difference between the ends of the film and the electrical conductivity was measured by the Van der Pauw method. The best hybrid film in this study exhibited a PF of 72 µW m−1K−2. These films are prepared from aqueous dispersions with relatively low-cost materials and, due to lightweight and flexible properties, they are potentially good candidates to recover waste heat in wearable electronic applications.