Energy-rich food wastewater (FWW) offers a sustainable feedstock for bioelectrochemical hydrogen production. However, its complex characteristics and high suspended solids content hinder its direct utilization in dual-chamber microbial electrolysis cells (MECs) for producing high-purity hydrogen. This study explored pre-fermentation under uncontrolled pH conditions as a method to improve the exoelectrogenic utilization of FWW in dual-chamber MECs. Across 2–5 d hydraulic retention times (HRTs), pre-fermentation was effective in conditioning FWW to a more favorable composition for exoelectrogenic utilization. Short-chain organic acids and ethanol constituted 48–72% of the total chemical oxygen demand (COD) in pre-fermentation effluents, a substantial increase from 27% in raw FWW. In subsequent MEC experiments, the MECs fed with pre-fermentation effluents exhibited significantly higher current-generating and hydrogen-producing performance compared to those fed with raw FWW. The MECs fed with the 2-d HRT pre-fermentation effluent showed the highest hydrogen yield of 911 mL/g COD fed, which represents a 34.4% increase compared to the MECs fed with raw FWW, resulting in a 1.28-fold higher recovery of chemical energy from organic matter in raw FWW as hydrogen. The anode bacterial community was dominated by exoelectrogenic Geobacter in all MECs, with its abundance being significantly higher when utilizing pre-fermentation effluents (69.0–78.0%) compared to raw FWW (20.6–39.2%). Overall, pre-fermentation proved an effective conditioning approach for enhancing the exoelectrogenic utilization of FWW in MECs.