The cyclability and the charge storage capacity of polymer electrodes prepared using potentiodynamic and potentiostatic electropolymerization techniques were studied. It was shown that potentiodynamically prepared films featured a much higher stability and reversibility of the doping–undoping processes approaching 100% over multiple cycles in comparison to potentiostatically prepared films. This was related to the difference in the nanoscale morphology, crystallinity and degree of disorder of polymer films, as evidenced by atomic force microscopy (AFM) and AFM phase imaging. Specifically, it was shown that potentiodynamically deposited films were more amorphous, which enabled the films to better withstand the mechanical stresses built up in the polymer phase due to repeated swelling–deswelling. The difference in the degree of disorder and crystallinity in polymer films prepared using potentiodynamic and potentiostatic methods were related to different concentrations and reactivities of oligomers generated in the electrode vicinity. Our results suggest that for charge storage applications, as opposed to solar cells and organic electronics, it is desirable to use the materials with an increased amorphous content.