We show how different supply chain configurations affect the economic performance and energy efficiency of biofuel supply chains. Despite the additional costs and energy required for installing and operating regional depots, transportation costs and energy savings are observed when depots are combined with the appropriate transportation modes at longer distances. We introduce a hybrid configuration which combines various configurations and leads to better economic performance and higher energy efficiency. We further study the impact of various factors on the performance of the biofuel supply chain: distance between harvesting site and depot, biomass productivity, biorefinery size, and densification efficiency. We show that biomass should be shipped directly to biorefineries when the distance is small, while depots are preferred at larger distances. The hybrid configuration offers lower minimum ethanol selling price and energy input for larger biorefineries. Furthermore, we study how improvements in densification technologies can reduce transportation cost and energy consumption.