The purpose of this study was to evaluate the current condition of palm oil mill effluent (POME) treatment and utilization and to propose alternative scenarios to improve the sustainability of palm oil industries. The research was conducted through field survey at some palm oil mills in Indonesia, in which different waste management systems were used. Laboratory experiment was also carried out using a 5 m3 pilot-scale wet anaerobic digester. Currently, POME is treated through anaerobic digestion without or with methane capture followed by utilization of treated POME as liquid fertilizer or further treatment (aerobic process) to fulfill the wastewater quality standard. A methane capturing system was estimated to successfully produce renewable energy of about 25.4–40.7 kWh/ton of fresh fruit bunches (FFBs) and reduce greenhouse gas (GHG) emissions by about 109.41–175.35 kgCO2e/tonFFB (CO2e: carbon dioxide equivalent). Utilization of treated POME as liquid fertilizer increased FFB production by about 13%. A palm oil mill with 45 ton FFB/hour capacity has potential to generate about 0.95–1.52 MW of electricity. Coupling the POME-based biogas digester and anaerobic co-composting of empty fruit bunches (EFBs) is capable of adding another 0.93 MW. The utilization of POME and EFB not only increases the added value of POME and EFB by producing renewable energy, compost, and liquid fertilizer, but also lowers environmental burden.