This paper describes a framework that can be used to evaluate the environmental risks and benefits associated with biofuel production. It uses the example of biodiesel produced from Argentinean soy to show how such a framework can be used to conceptualize trade-offs between different environmental, social and economic impacts of biofuel production. Results showing the greenhouse-gas savings and overall life-cycle impact of different ‘soy-biodiesel’ production methods are presented. These impacts and the significance of uncertainty in overall assessments of key parameters, such as greenhouse-gas savings, are discussed. It is shown that, even where sufficient knowledge exists to be able to quantify these impacts, the sustainability of supply of a particular biofuel is inextricably linked to values and ethical judgements. However, tailoring certification efforts to the issues that are most likely to make a significant difference to the overall sustainability could improve the effectiveness of certification efforts. The potential for a framework to guide and focus certification efforts is discussed and future research and policy priorities suggested.