The thermal stability of electrochemically prepared polypyrrole (PPy) films with p-toluenesulfonate (pTS) or perchlorate (ClO4−) counterion (PPy/pTS and PPy/ClO4−) is improved by simple treatment with aqueous sulfuric acid, sodium sulfate or sodium bisulfate. The degree of stabilization achieved depends on the solution, temperature and duration of treatment. Although the mechanism for improved stability is not yet clear, it is apparent that the level of ion exchange and the original polymer microstructure are important. A model for the conductivity decay as a function of thickness has been proposed. The early stages of ion exchange are not symmetrical, and diffusion is facilitated at the electrode side of the film. Furthermore, X-ray diffraction shows no evidence of morphological change after treatment of PPy/pTS (43 μm), but in PPy/pTS (12 μm) and PPy/ClO4− (41 μm) films an additional peak is indicative of more ordered structure following treatment. The glass transition temperature, Tg, of PPy/pTS and PPy/ClO4− films obtained by modulated differential scanning calorimetry is approximately 155°C.