This article analyzes the transition towards second-generation (2G) biofuels during the 2005–2018 period in Brazil, which is a world leader of first-generation (1G) biofuels. In the case of Brazil 2G technologies are associated with sugarcane and the technologies of this transition considered in this article are enzymatic hydrolysis and energy cane. The analytical background used is the technological innovation systems (TIS) framework. The functioning of the innovation system is studied using scientific papers, patents, reports, newspaper information, and other data from Brazilian funding agencies. The paper examines how the functions of the Brazilian bioethanol TIS related to 2G biofuels operated and were interconnected in this period. We found that the knowledge development and resource mobilization functions operated positively but others did not, especially guidance of the search, market formation and creation of legitimacy, revealing an unbalanced system transformation. During this period there were two important phases, one dominated by academic actors and the other by the federal development bank. However, we found that the functions were not enough to explain the TIS evolution, and that the external context of the global TIS and the Brazilian macroeconomic dynamic were also very important to explain this evolution. We conclude that the transition was not completed and that in the future policies should consider system dynamics and context evolution.