Although the decentralized and centralized strategies are widely known in today's supply chain realm, few studies have investigated their impacts on the bio-based waste management context. This study aims to formulate a multi-echelon structure for evaluating the influence of these supply chain strategies on optimal utilization of the biomass feedstocks. The proposed supply chain models, connecting the economic, social, and environmental aspects, tend to lower the total system costs, reduce the inadvertent effects of transportation and production processes, and respond to dynamic demands. The optimization problem is formulated as a mixed-integer linear programming model using generalized disjunctive programming to select the most robust integrated supply chain strategy. The results indicate that, although the centralized model leads to higher investment and operating costs than the decentralized model, centralization is still a more profitable alternative as well as being capable of the production of a broader portfolio of bio-based products.