Certification for biofuels has been developed to ensure that biofuel production methods adhere to social and environmental sustainability standards. As such, requiring biofuel production to be certified has become part of EU policy through the 2009 renewable energy directive (RED), that aims to promote energy security, reduce emissions and promote rural development. According to the EU RED, in 2020 10 % of our transport energy should come from renewable sources, most of which are expected to be biofuels. In this paper I examine what biofuel certificates are, what they can achieve and what their limitations are. Methodologically, I will evaluate them using the standards of instrumental, practical and communicative rationality. With regard to instrumental rationality, I conclude that the EU RED makes an important but unjustified assumption in demanding certified biofuels for its target: that if biofuel production is sustainable, then biofuel use is too. I also argue that, where the EU assumes that biofuel certification is a sufficient means to achieve the EU RED’s goals, it is at best an insufficient means and at worst not a means at all towards achieving these goals. With regard to practical rationality, I argue that more attention needs to be paid to trade-offs between different goals in the EU RED, particularly with regard to providing investor security and not capping transport energy consumption. With regard to communicative rationality, I argue that the policy-making process of the EU RED has been seriously flawed, and that certification development processes also can improve significantly.