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Polygeneration facilities, such as the integrated biorefinery, have the opportunity to provide a strong, self-dependent, sustainable alternative for the production of bulk and fine chemicals, e.g. polymers, fiber composites and pharmaceuticals as well as energy, liquid fuels and hydrogen. Although most of the fundamental processing steps involved in these polygeneration facilities are well-known, there is a need for a methodology capable of evaluating the integrated processes in order to identify the optimal set of products and the best route for producing them. The complexity of the product allocation problem for such processing facilities demands a process systems engineering approach utilizing process integration and mathematical optimization techniques to ensure a targeted approach and serve as an interface between simulation work and experimental efforts. The objective of this work is to assist potential and existing polygeneration facilities in evaluating the profitability of different possible production routes and product portfolios while maximizing stakeholder value through global optimization of the supply chain. To meet these ends, a mathematical optimization based framework is being developed, which enables the inclusion of profitability measures and other techno-economic metrics along with process insights obtained from experimental as well as modeling and simulation studies.