Abstract The efficiency of microbial electron transfer is fundamental for determining the performance of fermentative hydrogen/methane production. To facilitate microbial electron transfer, conductive magnetite nanoparticles (MNPs) were added into a cascading dark fermentation and anaerobic digestion system that was inoculated with Enterobacter aerogenes ZJU1 and methanogenic activated sludge (MAS), respectively. During the hydrogen-producing stage, the ratio of NADH/NAD+ and the activities of hydrogenase and electron transport system (ETS) of E. aerogenes ZJU1 were all increased by dosing 200 mg/L MNPs, which was conducive to hydrogen production through the NADH-dependent pathway. In the presence of 200 mg/L MNPs, hydrogen production increased by 21.1%, while subsequent methane production improved by 22.9%. Electrochemical analysis demonstrated the improvement in extracellular electron transfer capacity of MAS after adding MNPs, which can be ascribed to the contribution of MNPs and electrochemically active extracellular polymeric substances (EPS) induced by MNPs, such as humic acid-like and fulvic acid-like substances. Bacteria Syntrophomonas and Archaea Methanosarcina were the dominating enriched syntrophic partners, and the expression of functional genes involved in CO2 reduction to methane pathway was found to increase. Therefore, a more efficient fermentative hydrogen and methane co-production system was established by improving microbial electron transfer with the addition of MNPs.