AbstractIonic liquid (IL) post‐treatment of poly(3,4‐ethylene dioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) thin films with ethyl‐3‐methylimidazolium dicyanamide (EMIM DCA), allyl‐3‐methylimidazolium dicyanamide (AMIM DCA), and 1‐ethyl‐3‐methylimidazolium tetracyanoborate (EMIM TCB) is compared. Doping level modifications of PEDOT are characterized using UV–Vis spectroscopy and directly correlate with the observed Seebeck coefficient enhancement. With conductive atomic force microscopy (c‐AFM) the authors investigate changes in the topographic‐current features of the PEDOT:PSS thin film surface due to IL treatment. Grazing incidence small‐angle X‐ray scattering (GISAXS) demonstrates the morphological rearrangement towards an optimized PEDOT domain distribution upon IL post‐treatment, directly facilitating the interconductivity and causing an increased film conductivity. Based on these improvements in Seebeck coefficient and conductivity, the power factor is increased up to 236 µW m⁻¹K⁻². Subsequently, a model is developed indicating that ILs, which contain small, sterically unhindered ions with a strong localized charge, appear beneficial to boost the thermoelectric performance of post‐treated PEDOT:PSS films.