AbstractOrganic materials for thermoelectric (TE) applications have attracted a fair amount of attention in recent years due to remarkable advances achieved in terms of their figure of merit, ZT: a value of 0.42 has been reported by for poly(3,4‐ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) films treated with dimethyl sulfoxide, while 0.25 has been obtained for PEDOT:Tosylate. In this study various PEDOT morphologies are investigated, considering both neutral and doped (bipolaronic) samples, by means of classical molecular dynamics, by taking advantage of a recently developed all‐atom force field. In the case of bare PEDOT, it is found that changing the distribution of chain lengths affects the thermal conductivity of neutral and doped samples in a different way: longer chain lengths result in higher conductivities in the neutral scenario, whereas an intermediate chain length gives the highest value in the bipolaronic case. The role of PSS in the bipolaronic state, as compared to the simpler case where the counterion is Cl−, is discussed.