In this work we study the effect of different synthetic conditions on thermal transport properties of poly(3,4-ethylenedioxythiophene) (PEDOT) by focusing in particular on the role of proton scavengers. To this aim, different PEDOT samples were generated in silico using a novel computational algorithm based on a combination of first-principles density functional theory and classical molecular dynamics simulations. The corresponding thermal conductivities were then estimated using the approach to equilibrium molecular dynamics methodology. The results show that the initial synthetic conditions strongly affect the corresponding thermal conductivities, which display variations up to a factor of ∼2 depending on the proton scavenger. By decomposing the thermal conductivity tensor along the direction of maximum chain alignment and the corresponding perpendicular directions, we attribute the thermal conductivity differences to the variations in the average polymer chain length λave. A dependence of the thermal conductivity with the polydispersity index was finally observed, suggesting a possible role of intercrystallite chains in enhancing thermal transport properties. By means of the Green-Kubo modal analysis, we eventually characterize the vibrational modes involved in PEDOT thermal transport and investigate how they are related to the thermal conductivity values of the samples.