Furanic and phenolic compounds are problematic compounds resulting from the pretreatment of lignocellulosic biomass for biofuel production. Microbial electrolysis cell (MEC) is a promising technology to convert furanic and phenolic compounds to renewable H2. The objective of the research presented here was to elucidate the processes and electron equivalents flow during the conversion of two furanic (furfural, FF; 5-hydroxymethyl furfural, HMF) and three phenolic (syringic acid, SA; vanillic acid, VA; 4-hydroxybenzoic acid, HBA) compounds in the MEC bioanode. Cyclic voltammograms of the bioanode demonstrated that electrochemical reactions in the biofilm attached to the electrode were negligible. Instead, microbial reactions (i.e., fermentation followed by exoelectrogenesis) were the primary processes resulting in the electron equivalents flow in the MEC bioanode fed with the furanic and phenolic compounds. The distribution of electron equivalents during the fermentation and exoelectrogenesis were further quantified for each of the five compounds. More than 50% of the SA, FF, and HMF electron equivalents were converted to current. In contrast, only 12 and 9% of VA and HBA electron equivalents, respectively, resulted in current production, while 76 and 79% remained in fermentation products without being further utilized in exoelectrogenesis. For all five compounds, it was estimated that 10% of the initial electron equivalents were used for fermentative biomass synthesis, while 2 to 13% were used for exoelectrogenic biomass. The proposed mass-based framework of substrate utilization and electron flow provides an important foundation for the simulation of bioanode processes to guide the optimization of MECs converting biomass-derived waste streams to renewable H2.