Organic thermoelectric materials are of great interest for development of flexible thermoelectric devices. Two crucial parameters namely conductivity and Seebeck coefficient apparently display a trade-off effect towards optimization of thermoelectric (TE) properties. Dopants normally increase the conductivity of PEDOT:PSS but Seebeck coefficient remains unaffected at around 15–18 µV K−1. In this work, pre-treatment using triflic acid to PEDOT:PSS solution is employed displaying simultaneous increase in conductivity of 1686 S cm−1 and Seebeck coefficient of 23.6 µV K−1. Mechanism of improvements are attributed to the increased order of long-range crystal packing as well as hopping between newly generated DOS. HRTEM and XRD data substantiated the improved crystallinity. Acid treatment induced change of conformation from coil like benzoid to linear quinoid structure as observed by Raman spectra, with increasing level of oxidation based on Raman and UV–vis–NIR spectra. The carrier concentration and mobility increased leading to the power factor of 94 µW m−1 K−2. Flexible thermoelectric generator (TEG) device is developed on PET film which generate thermovoltage of 2.0 mV at temperature difference of 15 K.