A mechanistic study on use of alternating potential (i.e. electrode polarity switching) in synthetic organic electrochemical method development using the IKA Electrasyn 2.0 is described. Unexpected product selectivity challenges revealed that alternating potential facilitated direct, rather than mediated, electrochemical benzylic C–H oxidation of toluene derivatives. Whilst constant potential irrespective of the direction of electrode polarity was expected, our in‐depth analysis revealed changes in the magnitude of applied potential with periodic switching of electrode polarity. These findings highlight an equipment engineering concern that is likely to influence and inform optimisation strategies for a wide range of synthetic organic electrochemical methods under development.