Waste managers struggle to comply with the European legislation that regulates the handling of organic waste. A waste management system that aims at recovering nutrients from the municipal organic waste generated in the Spanish region of Cantabria was modeled by combining material flow analysis, life cycle assessment, and life cycle costing. The model was optimized to find system configurations that minimize the total annual cost (TAC) and the global warming impacts (GW) and maximize the circularity indicators of nitrogen and phosphorus (CIN and CIP). The developed superstructure is composed of waste management unit processes and unit processes related to the land application of the recovered products (compost, digestate, (NH4)2SO4, and NH4MgPO4·6H2O) and industrial fertilizers to grow corn. The results of the optimization indicate that increasing CIN and minimizing GW raises the TAC, because of the investment in new technologies, although high CIP values can be achieved at low TACs. The economic margin that enables the organic fertilizers to compete in the market with industrial fertilizers was estimated. Cooperation between waste managers, the farmers that purchase the recovered products, and the policy-makers that set the waste management taxes can minimize the costs that hinder the transition toward a circular economy.