Embrapa Agroenergy was created on May 24, 2006, with the beginning of the National Program of Biodiesel Production and Use (PNPB) and the launching of the National Agroenergy Plan (PNA), with objectives to ensure the increase of the participation of renewable sources in the National Energy Balance. In line with what was established in the PNA itself, research projects were established for Embrapa Agroenergy within the four axes: ethanol, biodiesel, energy forests, and by-products and residues. These projects aimed at the full utilization of the biomass from crops included in the agroenergy production chain, having in mind sustainability in its three pillars: environmental, economic and social, especially with biofuels. The first years (May/2006 to September/2011), led by researcher Frederico Ozanan Machado Durães, were marked by this research approach and the search for financial resources for the first projects. It was also the period of structuring of Embrapa Agroenergy, with the hiring of staff, acquisition of equipment and construction of the building that now houses the offices and laboratories.

In the second phase (September/2011 to October/2016), led by researcher Manoel Teixeira Souza Júnior, the Unit continued to invest in research focused on the production of biofuels, either in processes and inputs for the industries, or in the diversification of raw materials available for the sector in Brazil. However, the development of technologies to produce chemicals and materials of renewable origin from biomass began to gain more strength, as the need to adopt the logic of biorefineries in the industries became more evident, in Embrapa, in the country and in the world. This stage was also marked by the completion of the Unit's infrastructure works and the inauguration of the laboratories and the pilot plant area, as well as the organization of internal work processes.

As a result of the path taken by Embrapa Agroenergy in its first ten years, the Unit expanded its activities to biomass chemistry and technology, without neglecting biofuels. Based on the global perspectives for bioeconomy development, on the research groups already established and on the results obtained at the Unit, Guy de Capdeville's management organized the actions in four axes: Biomass for industrial purposes, Industrial biotechnology, Chemistry of renewables, and Renewable materials. The vision for the period was "to be a national and international reference in the generation of technological innovations that allow converting diversified renewable raw materials, by biochemical, chemical and thermochemical processes, into sustainable alternatives of bioproducts and bioenergy within the context of Industrial Biotechnology and Green Chemistry.

The fourth management of Embrapa Agroenergy began on February 7, 2020, when the then head of Technology Transfer, Alexandre Alonso Alves, became interim head of the Unit after Guy de Capdeville became Embrapa's Executive Director of Research and Development. In the first year of his management (February/2020 - February/2021), the UD had as a great challenge to plan and execute a prevention/remote work/relay plan for employees as a consequence of the Covid-19 pandemic. At the same time, it intensified institutional relationship actions and strategic positioning through the organization and participation in events/commissions/missions in order to consolidate the Unit in the biofuels and bioproducts thematics. In R&D, we highlight the implementation of nine projects and the approval/contracting of new innovation projects, two with resources from the Embrapa Management System ( SEG) and four through the Embrapii Biochemistry of Renewables unit. The capture of extra National Treasury resources allowed the improvement of the UD's infrastructure and the consolidation of actions with canola. In Technology Transfer, we highlight the creation of a business plan for the BtRR Sugarcane, resistant to the borer and glyphosate herbicide, besides the filing of three patents and a cultivar protection request at INPI. In the administrative area, the ERP/SAP system went into operation, integrating the administrative sectors with the final areas, resulting in greater operational efficiency.