In this study, the effects of indirect voltage supply to an anaerobic digestion (AD) reactor on methane production and the removal of chemical oxygen demand (COD) were studied at different organic loading rates (OLRs) of food waste by the circulation from an auxiliary bio-electrochemical reactor (ABER) with stainless steel (STS304) electrodes. The effects of the indirect voltage on microbial communities in the AD reactor were also investigated. In a bio-electrochemical anaerobic digestion (BEAD) reactor with direct voltage, it was possible to achieve stable COD removal and methane production even at a higher OLR of 10.0 kg/(m·d). However, in the AD reactor, the COD removal efficiency and methane production decreased sharply at an OLR of 6.0 kg/(m·d) due to the accumulation of volatile fatty acids (VFAs) and decreases in the pH and alkalinity. The supply of indirect voltage through the ABER increased the community of exoelectrogenic bacteria and hydrogenotrophic methanogens in the AD + ABER bulk solution. As a result, rapid oxidation of the accumulated VFAs occurred, and methane production increased in the new AD + ABER system. The results confirm that an indirect voltage supply to the new AD + ABER system can have effects similar to those of a direct voltage supply to the BEAD reactor, and the findings are expected to provide useful information for the development and application of BEAD technology for commercialization.