Dairy operations constitute ∼2.5% of annual U.S. greenhouse gas (GHG) emissions, making dairies one of the largest sources of industrial GHG emissions. We are developing a novel, integrated system to achieve a net reduction in dairy GHGs while producing value-added materials and products. This integrated manure-to-commodities system converts dairy manure to bioenergy, sequesters carbon by converting volatile fatty acid-rich fermenter supernatant to bioplastics, and utilizes anaerobic digester (AD) and polyhydroxyalkanoate (PHA) reactor effluents to produce algae that can be harvested and internally recycled to enhance PHA production and sequester carbon. A decision-making tool is being developed for the integrated system that quantifies net GHG reduction, carbon sequestration, nutrient management and economics.