This analysis estimates the cost of selected oil and biomass supply shocks for producers and consumers in the light-duty vehicle fuel market under various supply chain configurations using a mathematical programing model, BioTrans. The supply chain configurations differ by whether they include selected flexibility levers: multi-feedstock biorefineries; advanced biomass logistics; and the ability to adjust ethanol content of low-ethanol fuel blends, from E10 to E15 or E05. The simulated scenarios explore market responses to supply shocks including substitution between gasoline and ethanol, substitution between different sources of ethanol supply, biorefinery capacity additions or idling, and price adjustments. Welfare effects for the various market participants represented in BioTrans are summarized into a net shock cost measure. As oil accounts for a larger fraction of fuel by volume, its supply shocks are costlier than biomass supply shocks. Corn availability and the high cost of adding biorefinery capacity limit increases in ethanol use during gasoline price spikes. During shocks that imply sudden decreases in the price of gasoline, the renewable fuel standard (RFS) biofuel blending mandate limits the extent to which flexibility can be exercised to reduce ethanol use. The selected flexibility levers are most useful in response to cellulosic biomass supply shocks.