Abstract This study presents a two-stage chance-constrained stochastic programming model that captures the uncertainties due to feedstock seasonality in a bio-fuel supply chain network. The chance-constraint ensures that, with a high probability, Municipal Solid Waste (MSW) will be utilized for bio-fuel production. To solve our proposed optimization model, we use a combined sample average approximation algorithm. We use the state of Mississippi as a testing ground to visualize and validate the modeling results. Our computational experiments reveal some insightful results about the impact of MSW utilization on a bio-fuel supply chain network performance.