Variations of physical and chemical characteristics of biomass lead to an uneven flow of biomass in a biorefinery, which reduces equipment utilization and increases operational costs. Uncertainty of biomass supply and high processing costs increase the risk of investing in the US?s cellulosic biofuel industry. We propose a stochastic programming model to streamline processes within a biorefinery. A chance constraint models system?s reliability requirement that the reactor is operating at a high utilization rate given uncertain biomass moisture content, particle size distribution, and equipment failure. The model identifies operating conditions of equipment and inventory level to maintain a continuous flow of biomass to the reactor. Furthermore, the sample average approximation method approximates the chance constraint and a bisection search-based heuristic solves this approximation. A case study is developed using real-life data collected at Idaho National Laboratory?s biomass processing facility. An extensive computational analysis indicates that sequencing of biomass bales based on moisture level, increasing storage capacity, and managing particle size distribution, increases utilization of the reactor and reduces operational costs.