Abstract This article describes the key challenges and opportunities in modeling and optimization of biomass-to-bioenergy supply chains. It reviews the major energy pathways from terrestrial and aquatic biomass to bioenergy/biofuel products as well as power and heat with an emphasis on “drop-in” liquid hydrocarbon fuels. Key components of the bioenergy supply chains are then presented, along with a comprehensive overview and classification of the existing contributions on biofuel/bioenergy supply chain optimization. This paper identifies fertile avenues for future research that focuses on multi-scale modeling and optimization, which allows the integration across spatial scales from unit operations to biorefinery processes and to biofuel value chains, as well as across temporal scales from operational level to strategic level. Perspectives on future biofuel supply chains that integrate with petroleum refinery supply chains and/or carbon capture and sequestration systems are presented. Issues on modeling of sustainability and the treatment of uncertainties in bioenergy supply chain optimization are also discussed.