The present article researches the mechanisms suggested for controlling the fulfillment of the EU sustainability criteria for transport biofuels that have been presented in the central legal framework in this area, which is Directive 2009/28/EC. The analysis is extended to the related EU policy documents of a non-binding explanatory and recommendatory character. Judging from the content of Directive 2009/28/EC, two main levels of the EU control can be distinguished. The first one is exercised by the EU internal bodies on how the sustainability criteria are fulfilled by the Member States. This level of control is primarily characterized by the scheduled reporting obligations of the Member States. The second level of control is aimed to take place within the Member States. The implication of Directive 2009/28/EC is that the Member States shall organize national systems, which control and are able to prove that biofuels, counted for the achievement of the national binding target in the transport sector, fulfill the legislated sustainability criteria. According to the suggested classification, the second level of control also includes meeting bilateral and multilateral agreements. What is more, the sustainability criteria in Directive 2009/28/EC can be counted as fulfilled, when similar sustainability criteria in voluntary sustainability standards benchmarked by the EU Commission are fulfilled.