To avoid negative outcomes of rising biofuel production and use, and to reduce simultaneously greenhouse gas emissions, the European Commission linked its mandatory biofuel blending requirements to sustainability criteria defined in the Directive on the Promotion of the Use of Energy from Renewable Sources (2009). Several voluntary, private standard initiatives are controlling the compliance along the value chain. Given that little experiences exist as to the certification of a large scale commodity like biofuels, there are many challenges to overcome. One point in question is the participation of small scale farmers in this complex and price bonded process. Is it possible to create methodologies to ensure the participation of smallholders? Additional uncertainties exist as to the implementation of control tools to avoid the jeopardizing of biodiversity or land with high carbon stocks. The objective of this study is to scrutinize the implementation of the sustainability criteria and its effects on crucial aspects as the inclusion of smallholder properties in certification schemes, effects on biodiversity or land use change. In addition, this work examines the possible limits of certification in the context of biofuel production and its claims for sustainable production patterns.