We focus on design and planning of a biofuel supply chain (SC) network from biomass to demand centers where biomass supply is stochastic and seasonal, and facilities’ capacity varies randomly because of possible disruptions. We propose a cost-efficient multi-stage stochastic program in which the greenhouse gas emissions are mitigated and the social impact of the SC is considered. A rolling horizon procedure is presented to implement and evaluate the stochastic model solution. Computational results on a real-life case study demonstrate the proposed optimization tools’ applicability as well as the effect of disruption risk and sustainability dimensions on biofuel SC planning.