The emerging bioeconomy offers numerous potential benefits, including development of carbon-neutral energy sources, energy independence, production of novel bioproducts, and renewal of rural economies. Aside from the benefits, the emerging bioeconomy is likely to result in the single largest reconfiguration of the agricultural landscape since the advent of industrial agriculture. The scale and pace of this revolution pose significant challenges for sustainable bioeconomic development. We present and explore some of the key ecological and environmental challenges of one aspect of the bioeconomy - biofuel production.