Prospective studies carried out by IPCC show that the quantity of biomass energy necessary to substitute fossil fuels has to quadruple by 2100 to achieve targets of reduction in atmospheric CO2 concentrations. The agriculture and forestry sectors are already extensively involved in energy production: electricity, heat, and solid and liquid fuels. Four major agri-chains in the countries of the South are active participants in such endeavours: those of oil palm, sugarcane, cassava, and timber. The energy market is becoming increasingly important in the organization and management of these sectors. It is already exerting considerable influence on agricultural practices, adaptation of planting material, land use modifications, and, in general, the management of flow of materials all through the production and processing stages. In the context of a growing demand for energy and of the growing presence of international actors in the energy supply chains, the sustainability of bioenergy production methods is not only a major challenge, but also imperative for any significant growth in energy production. In order to address this challenge, the agri-chains are, on the one hand, developing sustainability standards and, on the other, continuing to leverage complementary aspects of the food, energy, and materials markets in order to avoid irreversible damage. Nevertheless, the use of biomass for energy remains controversial and several questions regarding its social and environmental impact remain to be answered. Paradoxically, little research has been conducted to design sustainable production systems on a large scale. A major reason is undoubtedly the lack of policy frameworks that define clearly the importance States wish to ascribe to biofuels in their energy mix and their agriculture.