For conductive polymers to be considered materials for energy storage, both their electroactivity and stability must be optimized. In this study, a non-aqueous electrolyte (0.2 M LiClO(4) in acetonitrile) was studied for its effect on the charge storage capacity and stability of two materials used in batteries developed in our laboratory, polypyrrole (pPy) and poly(3,4-ethylenedioxythiophene) (PEDOT) doped with 2,2'-azino-bis(3-ethylbenzothiaxoline-6-sulfonic acid (ABTS). The results are compared to the performance of these materials in an aqueous electrolyte (0.2 M HCl/aq). Loss of ABTS dopant was eliminated principally due to the low solubility of ABTS in acetonitrile, resulting in cathode materials with improved stability in terms of load cycling and performance.