The processes occurring during the electrochemically irreversible reduction of flavins in aprotic organic medium have been the cause of considerable controversy. To provide insight into these events we have investigated the reduction of flavins alkylated at N(3). We have demonstrated that the reversible reduction of N(3)-methylated flavin can be converted to the irreversible reduction observed with unalkylated flavins through addition of the weak external proton donor phthalimide. Proton transfer to the flavin radical anion generated at the electrode leads to partial formation of the neutral flavin radical; which is instantaneously further reduced to the fully reduced flavin anion. This mirrors the reduction of unalkylated flavins, where the proton source is the imide proton at N(3) of fully oxidized flavin in bulk solution. Simultaneous electrochemistry and EPR experiments confirm the disappearance of electrogenerated flavin radical anion both methylated and non-methylated at N(3), upon addition of phthalimide. UV/vis spectroelectrochemistry likewise confirmed the generation of the radical anion in the absence of proton donors and fully reduced flavin in the presence of proton donors.