The electrochemical quartz crystal microbalance (EQCM) technique was used to investigate the electrochemistry of neutral red (NR) in phosphate buffer solution (PBS) and the effects of coexisting heparin (Hep) or chondroitin sulfate (CS) for the first time. The pH dependence of the electrochemistry of NR was examined, and a V-shaped frequency response (versus time) was observed during the cyclic voltammetric experiment of NR in a nearly neutral medium (pH ca. 6.10–7.00), being due to the electrodeposition and stripping of the poorly soluble reduced product of NR (NR Red ) at these pH values. The effects of potential scan rate, the concentration of NR, and several supporting electrolytes were examined at pH 6.80. The V-shaped response to the redox switching of NR was weakened by the introduction of Hep or CS, being due to the increased inhibition of the NR Red electrodeposition probably via the electrostatic interaction of the NR and especially the NR Red with Hep or CS. The height of the V-shaped response decreases with the increase of Hep or CS concentration, with limits of detection down to 3nmolL −1 for Hep and 2nmolL −1 for CS, respectively. The novel and surface-regenerable EQCM assay protocol based on the electrochemically switchable deposition of a dye is highly recommended for wide biosensing applications.