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The present work proposes a computer-aided methodology for designing sustainable supply chains in terms of sustainability metrics by utilizing the P-graph framework. The methodology is an outcome of the collaboration between the Office of Research and Development (ORD) of the U.S. EPA and the research group led by the creators of the P-graph framework at the University of Pannonia. The integration of supply chain design and sustainability is the main focus of this collaboration. The P-graph framework provides a mathematically rigorous procedure for synthesizing optimal and alternative suboptimal networks subject to multiple objectives and constraints, which include profitability and sustainability in the proposed methodology. Specifically, to evaluate the sustainability of a given process under construction including its supply chain, sustainability metrics are incorporated into the design procedure. The proposed methodology is demonstrated with the optimal design of a supply chain for providing heat and electric power to an agricultural region with relatively limited land area where agricultural wastes can potentially be recovered as renewable resources. The objective functions for optimization comprise the profit and the ecological footprint. The results of the study indicate that, compared to using electricity from the grid and/or natural gas, using renewable energy resources can yield substantial cost reductions of up to 596, as well as significant ecological footprint reductions of up to 77%. It may, therefore, be possible to design more sustainable supply chains that are both cost-effective and less environmentally damaging.