Integration of microbial electrolysis cell (MECs) is a novel, promising, and economically feasible technology used to produce methane during the second stage (Dhar et al., 2015). In such process, hydrolysis, and acidogenesis take place during the first stage at optimal pH of 5–6 and HRT 1–3 days while the remaining organics of the first stage i.e. hydrogenic effluent was converted anaerobically into methane via methanogenesis under optimal HRT and pH range of 10–20 days and 7–8, respectively (Krishnan et al., 2016). Mamimin et al. (2015) achieved continuous hydrogen and methane yield of 210 L H2 kgCOD-1 and 310 L CH4 kgCOD-1, at feed rate of 60gCODL-1d-1 using CSTR-UASB reactor at thermophilic temperature (55 °C). MEC is a device that can convert organic acetic and butyric acid to methane gas through microbial electrolysis process (Bo et al., 2014). In MECs, microbial biofilm attached to anode acts as an electron donor, which oxidizes organic waste/or effluent, thereby releasing electrons to cathode through an extracellular circuit, where cathode respiring bacteria (like methanogens) and catalyse methanogenesis by reducing electron acceptor like CO2 to produce methane (Pisciotta et al., 2012). This new concept eventually helps to improve gaseous energy recovery. Few studies have revealed higher degradation rates of various types of substrates in a conventional single stage MEC system. Using MEC, Sun et al. (2015) observed an increase from 11% to 32% in the total COD removal from waste-activated sludge at a concentration of 10 g COD L−1. However, hydrogen production coupled with MEC is highly influenced by various physicochemical factors including pH, electric voltage, substrate type, temperature, HRT, OLR, and reactor configuration. These parameters need optimisation for effective microbial metabolic balance and subsequently the fermentation end products.Palm oil mill effluent (POME) is a major environment threatening effluent in chief oil palm producing nations like Indonesia, Malaysia and Thailand. It is estimated that palm oil mill in Malaysia and Indonesia discharges around 60 million m3 which has a potential to generate power equivalent of 850 GW (Lamaming et al., 2015). POME has high organic content which is normally discharged at high temperatures around 60 to 70 °C. Therefore, thermophillic dark fermentation is preferably more suitable method for its treatment than other available methods in order to achieve dual benefit of energy recovery and waste stabilization. However, there is still a lack of information for optimised two-stage process to treat POME, especially for continuous operation. Based on the above information, we herein developed a two-stage bioprocess combining thermophilic hydrogen production CSTR reactor and a mesophilic methane production MEC reactor. The objective of the present work is to examine the hydrogen and methane production potential of the POME using a two-stage thermophilic dark fermentation and mesophilic MECs approach at different HRTs (4–12 days) and voltages (0.1–0.8 V). The continuous operation of two-stage reactors was monitored, optimised, and microbial consortia inside both bioreactors were analysed for its practical operation for three months in terms of stable hydrogen and methane gas production. This integrated approach is a feasible, low cost and effective treatment technology for industrial wastewater stream with coproduction of bioenergy resources like hydrogen and methane.