By means of biorefinery, biogas production through anaerobic digestion is one of the most common treatments of wastewater in the palm oil industry. After biogas production, the treated palm oil mill effluent (POME) is generally discharged into the environment. However, certain level of hazardous compounds still exists in the treated wastewater, which can lead to the pollution of water bodies. In this study, we have investigated the dynamics of volatile organic acids dwelling in consecutive POME treatment lagoons as well as identified, and categorized, microbial species responsible for the treatment process. Bacteria and methanogens, both hydrogenotrophic and acetoclastic, related to methane production were identified using mcr A and 16S rRNA genes specific primers. Two hydrogenotrophic methanogens, Methanoculleus marisnigri and Methanoculleus chikugoensis , were found abundant in accordance with high formate concentration throughout the process of anaerobic digestion. This study has also isolated eight consortia of microbes that yielded different methane productions by utilizing formate as the substrate in the synthetic medium. The consortia of a group, containing M. marisnigri , M. chikugoensis , uncultured bacteria , Aminobacterium sp. , and Ruminobacillus xylanolyticum , produced the highest methane yield of 259 mL/g COD after 25 days of incubation in the laboratory. The findings from this study are contributing to optimize and increase biogas production in POME, which will allow higher efficiency in palm oil mill wastewater treatment.