The increase in water pollution from nutrients like phosphorus and nitrogen has prompted the Philippine government to issue stringent regulatory standards for wastewater effluent quality. Hence, two alternatives are being proposed to be integrated in the current wastewater treatment plant in the Philippines: biological nutrient removal and nutrient recovery systems. Biological nutrient removal technologies (BNRT) utilize microorganisms to minimize the nutrient content in the effluent streams to the standard limit while leaving high nutrient concentrations to the sludge that is typically transported as waste to landfill. The nutrient recovery system aims to recover phosphorus and nitrogen in the form of struvite (NH4MgPO4·6H2O) fertiliser from sludge through chemical precipitation. The two proposed systems have been studied in other settings but their effectiveness has not been studied in the Metro Manila setting. There is a need to systematically assess the environmental effects brought about by the proposed systems in Metro Manila, whether beneficial or adverse, in the context of agriculture, food and energy consumption, and wastewater. A holistic evaluation of the environmental benefits and burdens was done using Life Cycle Assessment (LCA) framework considering a cradle-to-grave approach of three scenarios: 1) current wastewater treatment system scenario; 2) biological nutrient recovery technology; and 3) nutrient recovery system. The environmental impact assessment was done using IMPACT2002+ methodology with the following impact indicators: human health, ecosystem quality, climate change and resources. The life cycle assessment of the scenarios shows the potential of the proposed retrofit wastewater systems for Metro Manila that extends to a more sustainable approach in dealing with issues such as water pollution, climate change, resource depletion and even food security. Moreover, a baseline understanding of the food-water-energy-nutrient nexus in the Philippines was established which can be the basis for future life cycle sustainability assessment studies.