A technoeconomic model has been developed to explore the viability of a two-stage anaerobic digester (AD) coupled with additional processes to increase the economic attractiveness of a new manure treatment system. The addition of a polyhydroxyalkanoate (PHA) reactor, algae cultivation system (ACS), and a biomass treatment system, such as, fast-pyrolysis or hydrothermal liquefaction (HTL) would further sequester carbon and nutrients, as well as add valuable products that can be sold or used on-site to mitigate costs. The Decision-support for Digester-Algae IntegRation for Improved Environmental and Economic Sustainability (DAIRIEES) model is used to evaluate the effectiveness and viability of this system to achieve economic and environmental sustainability by the dairy industry. The DAIRIEES model was used to evaluate the effectiveness and viability of this system to achieve economic viability and environmental sustainability by the dairy industry. A base case with mass flows and economics for a 10,000 herd dairy is considered. The integrated manure treatment system can reduce the amount of nitrogen released from the manure by 61.7%. If the ACS is not incorporated into the system, the nitrogen reduction drops to 19%. Similarly, the amount of phosphorus available for release to the environment is reduced by 37.4% with the full system, and by 26% for the system without the ACS. The results of the economic analysis indicate a net loss for the integrated system with algae cultivation. Without algae cultivation, the manure treatment system is profitable with a payback period of less than five years.