Chemical and electrochemical doping of π-conjugated polymers is an important aspect in determining the performance and enabling the operation of many organic electronic devices, from organic light emitting diodes and thermoelectrics to organic electrochemical transistors. In both chemical doping and electrochemical doping an ionized dopant or counterion is present along with the doped π-conjugated polymer. This dopant or counterion is not a benign spectator, rather, its presence can significantly impact the optical, electronic, and thermoelectric properties of the resulting material. Here, we investigate how counterion structure impacts the electrochemical doping ability, oxidation potential, ionization energy, and polaron absorbance of regioregular (rr) and regiorandom (rra) P3HT. We find that in most cases the anion has a small effect on the polymer oxidation potential, except for in the case of rr-P3HT with the large tetrakis[3,5-bis(trifluoromethyl)phenyl]borate anion. We propose that this large anion is excluded from the crystalline regions and thus the oxidation potential is similar to that of rra-P3HT. The anions also result in significant differences in polaron absorbance and ionization energies, thereby emphasizing the important role of the counterion in determining the optical and electronic properties of doped π-conjugated polymers.