Anaerobic microorganisms use flavin/quinone-based electronic bifurcation (EB) to gain a survival advantage at the thermodynamic limits. However, the contribution of EB to microscopic energy and productivity in the anaerobic digestion (AD) system is unknown. This study demonstrates for the first time that under limited substrate conditions, Fe-driven EB in AD leads to a 40% increase in specific methane production and contributes to 25% ATP accumulation, by analyzing the concentration of EB enzymes such as Etf−Ldh, HdrA 2 B 2 C 2 , and Fd, NADH and actual Gibbs free-energy changes. Differential pulse voltammetry and electron respiratory chain inhibition experiments detected that iron enhanced electron transport in EB by accelerating the activity of flavin, Fe−S clusters, and quinone groups. Other microbial and enzyme genes with EB potential closely related to iron transport have also been found in metagenomes. The potential of EB to accumulate energy and enhance productivity in AD systems was investigated, and metabolic pathways were proposed in the study.