Polymer-based electrodes for interfacing biological tissues are becoming increasingly sophisticated. Their many functions place them at the cross-roads of electromaterials, biomaterials, and drug-delivery systems. For conducting polymers, the mechanism of conductivity requires doping with anionic molecules such as extracellular matrix molecules, a process that distinguishes them as biomaterials and provides a means to control interactions at the cellular–electrode interface. However, due to their complex structure, directly observing the selective binding of target molecules or proteins has so far eluded researchers. This situation is compounded by the polymer's ability to adopt different electronic states that alter the polymer–dopant interactions. Here, the ability to resolve sub-molecular binding specificity between sulfate and carboxyl groups of dopants and heparin binding domains of human plasma fibronectin is demonstrated. The interaction exploits a form of biological ‘charge complementarity’ to enable specificity. When an electrical signal is applied to the polymer, the specific interaction is switched to a non-specific, high-affinity binding state that can be reversibly controlled using electrochemical processes. Both the specific and non-specific interactions are integral for controlling protein conformation and dynamics. These details, which represent the first direct measurement of biomolecular recognition between a single protein and any type of organic conductor, give new molecular insight into controlling cellular interactions on these polymer surfaces.