For electrified surfaces, ions and applied potentials play major roles in controlling the surface properties. Antifouling materials such as poly(ethylene glycol) and zwitterionic polymers that resist nonspecific protein binding and cell adhesion play a key role in various biomedical applications. In this study, we investigated and compared the antifouling properties of conducting polymers grafted with oligo-(ethylene glycol) groups and phosphorylcholine (PC) groups in the presence of different anions and applied potentials. Considerable effort has been made to illustrate the different effects of manipulating the antifouling properties of these two surfaces. We prepared polymer films by applying electropolymerization to two functionalized (3,4-ethylenedioxythiophene) polymers containing triethylene glycol and PC groups, respectively. A quartz crystal microbalance with dissipation (QCM-D) was employed to characterize the negatively charged bovine serum albumin and positively charged lysozyme adsorption as a function of ionic concentration in the presence of various Hofmeister anions. The frequency changes corresponded to the protein or ion adsorption/desorption behavior on the surface. The anions adsorbed on polymer films to effectively enhance the hydration layer of the polymer surface and reduce nonspecific protein binding. We further integrated a potentiostat with the QCM-D to control the protein adsorption/desorption behaviors by applying potentials, and we conducted an electrochemical QCM-D study. Most importantly, with the synergistic effect of ions and surface potential, a nearly fresh polymer surface was regenerated. This study describes principles to maintain and regenerate the antifouling properties of electrified surfaces, which are critical for implanted bioelectronics applications.