The uses of quinones in Redox Flow Batteries (RFBs) has been mainly circumscribed to aqueous solutions (of derivatives with polar groups) despite a larger solubility and wider electrochemical window provided by organic media. The redox mechanism of quinones in protic media is simpler and better known than in aprotic media, where radical species are involved. This paper reports the behaviour of methyl-p-benzoquinone (MBQ) under electrochemical reduction conditions in a LiClO4 CH3CN electrolyte and various working electrodes. We detected the reversible generation of a bright green coating on the working electrode and the subsequent formation of a polymer (the nature of which depends on the presence or absence of oxygen). These coatings prevent the regular redox process of methyl-p-benzoquinone from taking place on the surface of the electrode and is generated regardless of the electrode material used or the presence of O2 in solution. In addition to MBQ, the green passivating layer was also found for less sterically hindered quinones such as p-benzoquinone or 1,4-naphthoquinone, but not for anthraquinone. We have also shown the central role of Li+ in the formation of this green layer. This work provides important guidelines for the final use of quinones in RFBs with organic electrolytes.