A concept is outlined for the production of materials/commodities from a polluting waste. A preliminary evaluation is presented for a proposed integrated dairy farm manure management system consisting of a two-stage anaerobic digester coupled with a polyhydroxyalkanoate reactor, algae cultivation system (ACS) and a biomass treatment system, such as fast-pyrolysis or hydrothermal liquefaction, to sequester carbon, nitrogen and phosphorus into value-added products (e.g., bioplastics, biogas, fertilizer, soil amendment and livestock bedding) rather than releasing them into the environment. Mass flows through the system are presented for a 10,000-cow dairy. The integrated manure treatment system can reduce the amount of nitrogen and phosphorus released from the manure by 50.9% and 38.1%, respectively. Without an ACS, the reduction drops to 19% and 27%, respectively. Greenhouse gas emissions can potentially be reduced by 44,200 MT CO2e/year over the referenced open lot dairy.