Ionic liquid (IL) post-treatment for thin films of poly(3,4-ethylene dioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) is employed for the simultaneous enhancement of Seebeck coefficients and electrical conductivities. Through systematic variation of the ILs, by changing the anions while keeping the cation unchanged, changes in thermoelectric, spectroscopic, and morphological properties are investigated by means of UV−vis spectroscopy and grazing-incidence wide-angle X-ray scattering (GIWAXS) as a function of the IL concentration. The simultaneous enhancement in the two important thermoelectric properties is ascribed to the binary nature of the ILs, which complements that of PEDOT:PSS. The anions of the ILs primarily interact with the positively charged, conducting PEDOT, while the cations interact with negatively charged insulating PSS. Therefore, post-treatment with ILs allows for primary and secondary doping of PEDOT:PSS at the same time. Differences in the obtained Seebeck coefficients for the investigated ILs are ascribed to the chemical properties of the anions. Additionally, the choice of the latter has implications on the morphology of the treated PEDOT:PSS films regarding average π−π-stacking distances of PEDOT chains, PEDOT-to-PSS ratios, and edge-on-to-face-on ratios, influencing charge transport properties macroscopically. A morphological model is presented, highlighting the influence of each IL in comparison with pristine PEDOT:PSS films.