Cyclic voltammetry, X-ray microanalysis (EDS), FTIR, and AFM were applied for the systematic examination of the influence of self-exchange and potential stimulated ion-exchange on the electrochemical properties of polypyrrole (PPy) films prepared in the presence of benzene sulfonate (BS), para-toluene sulfonate (pTS), and naphthalene-1, 5-disulfonate (NDS) anions. All electrochemical experiments were carried out in aqueous solutions. It was established that small inorganic anions, like NO3−, Cl−, ClO4− can relatively easily replace an essential part of the sulfonates in PPy/BS and PPy/pTS films simply during a 10min polarization at 0.4V. A single potentiodynamic cycle increases the completeness of the exchange of the anions remarkably. The EDS analysis carried out before and after the anion exchange showed that 5–15% of the sulfonate anions still remain in the PPy films. The ability of the double-charged SO42− anions to replace sulfonate anions is even more pronounced as the exchange process does not need additional electrochemical activation. The quantum chemical model calculations have shown that the interaction of the sulfate anions with charged pyrrole oligomers is essentially stronger compared to other anions under the study.The redox capacitance and the corresponding electrochemical doping level of the redoped PPy films are remarkably higher than those before ion-exchange, showing that the PPy matrix formed in the presence of sulfonate anions does not collapse after ion-exchange and it creates favorable conditions for increased mobility of inorganic anions.