The growing utilization of biomass feedstocks for climate change mitigation has led to increased research on biorefineries. Concurrently, environmental policies are evolving as crucial tools to address these global concerns. Cap-and-trade, carbon tax, and carbon cap policies have been established to reduce carbon dioxide emissions. In this work, a mathematical optimization model is developed to integrate biorefinery process design with carbon pricing policies and crediting mechanisms. A two-stage stochastic mixed integer linear programming model is proposed to account for emissions, feedstock supply, chemical demand, and pricing uncertainties. A bi-objective optimization framework is employed to consider economic and environmental metrics. The framework is a valuable tool for governments and businesses to determine pareto-optimal investment strategies under environmental policies. It is applicable for evaluating prospective chemical technologies with carbon pricing policies beyond biorefineries. The results indicate that carbon crediting mechanisms can minimize the financial penalty by up to 50% under a carbon tax policy. Implementing chemical demand constraints within a cap-and-trade policy reduces potential profits, especially when the carbon prices are high. The stochastic programming approach revealed that underestimating the expected carbon cap leads to lower expected profits. Despite the financial implications of these policies, profitable process designs are achievable.