Palm oil milling by-products including palm oil mill effluent (POME) are generated abundantly during operation and processing of fresh fruit bunches in mills which cause disposal issues if untreated. While anaerobic digestion and presently employed tertiary treatment technologies of POME are able to meet the current regulated biological oxygen demand (BOD) discharge limit of 100 mg/L, most of the POME treatment technologies in use are found inconsistent in their performance. We investigated the possibility of integrating several bio-processes mainly routed in ‘pre-treatment-biological process–membrane separation’ to treat POME which could transform the POME into several value-added products, i.e. bio-fertilizer (as compost for crops cultivation), biogas (as renewable energy source) and recycled water (as boiler grade water) with BOD <20 mg/L attainable at its final discharge. As the treated POME exhibits substantial NPK nutrients, with presence of volatile fatty acid from <0.58 g/L to the maximum 2-fold allowable concentration and oil & grease ranged 9.3 mg/L–18.4 mg/L, it can be conditionally used as a low-cost alternative to complement the widely used chemical fertilizers. The findings of this study offer a potential waste-to-wealth integrated approach using a locally available agricultural by-product (POME), maximizing resource recovery in producing biogas, recycled water and organic fertilizer, in meeting food-energy-water nexus resources demand and conserving the environment for a circular economy.