Aerosol-jet printing allows functional materials to be printed from inks with a wide range of viscosities and constituent particle sizes onto various substrates, including the printing of organic thermoelectric materials on flexible substrates for low-grade thermal energy harvesting. However, these materials typically suffer from relatively poor thermoelectric performance, compared to traditional inorganic counterparts, due to their low Seebeck coefficient, S, and electrical conductivity, σ. Here, we demonstrate a modified aerosol-jet printing technique that can simultaneously incorporate well dispersed high S Sb2Te3 nanoflakes, and high-σ multi-walled carbon nanotubes (MWCNTs) providing good inter-particle connectivity, to significantly enhance the thermoelectric performance of poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) structures on flexible polyimide substrates. A nominal loading fraction of 85 wt.% yielded a power factor of ~41 µW/mK2, which is among the highest for printed organic-based structures. Rigorous flexing and fatigue tests were performed to confirm the robustness and stability of these aerosol-jet printed MWCNT-based thermoelectric nanocomposites