With the race to find and exploit new gas and oil resources, biofuels may become irrelevant. These global trends undercut efforts towards an energy transition in which clean energy could be important. The high financial and environmental costs that result from exploiting old and new sources of oil and gas as well as the potential that biofuels can have a positive impact on inclusive socio-economic development may be ignored. Agriculture is a key link between clean energy and inclusive development for producing biodiesel made from seeds of oil-rich plants, and ethanol from sugarcane or maize. However, biofuels have been praised for providing energy and reducing greenhouse gas emissions, and criticised for contributing to the destruction of tropical forests and competing with food crops. The negative effects need not always result. Jatropha, for example, can grow on marginal land and in arid environments but, it has not worked out well everywhere; the case of Garalo in Mali being an exception. In 2007, the villagers of Garalo decided to plant 440ha of jatropha as part of a multi-goal project to reduce dependence on imported diesel and stimulate rural development by providing electricity for meeting various needs. However, the long time to maturity of jatropha seed, meant that four years later, jatropha oil accounted for only 5-10% of the fuel needed. Nonetheless, the project produced some positive results. For example, after two years, many farmers had chosen to intercrop jatropha and local food crops such as cereals and beans, indicating that an either-or choice between using land for food or fuel is not essential. The farmers also developed close links to research institutions which resulted in joint experimentation and local learning as well as improved production systems. Such learning processes and linkages offer the flexibility that smallholder farmers need to adapt as prices and competitive conditions change. A women’s group in Gbimsi, in Northern Ghana, created such linkages in the early phase of project development. They normally took two weeks to process 25 kg of shea butter, because of lack of energy. With support from the Ghana Regional Appropriate Technology Industrial Service and UNDP-GEF, they grew jatropha on a 4-ha farm, extracted the oil using equipment designed by the GRATIS Foundation, mixed it with traditional diesel (70:30) and operated their equipment. Within a few years, they were producing 1 tonne shea butter in a month and earning two million Ghana cedis (around US$ 1 million) in profit. Most jatropha projects have not put farmers in the driver’s seat, nor adopted the kind of multi-goal approach that strengthens smallholder farmer communities. This is particularly true when from the outset Jatropa oil is produced for export with unexpected, often negative impact on inclusive development. Firstly, jatropha is not a low-cost, low-input crop that can grow virtually by itself. Growing jatropha requires costly upfront investments in improved seeds, water and fertiliser and a long period before the shrub is mature. This puts it in direct competition with staple food crop production. Jatropha projects are mostly undertaken by foreign investors on purchased or leased land. Failure to reach anticipated yield levels in a reasonable timeframe and changes in global pricing for fuels have led to the abandonment of many such ventures. Secondly, mass market and export activities require a quite different management, and ownership model. This limits the role of jatropha in local development, especially for smallholders. A broad range of other agricultural-plant-based inputs that can be used to produce diesel fuel exists and the amount of oil that can be extracted should be considered. Sunflower seeds and rapeseed oil, for example, are high in extractable oil (43% and 40%, respectively). This increases their energy efficiency in biodiesel engines. In transitioning to clean and renewable energy, the pros and cons of each option need to be considered within the local context. In the not-too-distant past, the very notion of building a bioeconomy in a developing country would have seemed unrealistic. Currently, however, the development of biofuels from sugarcane and second generation cellulosic ethanol and diesel and the ongoing research on enzymes to decompose wastes and make diesel fuel from algae, suggest that this is no longer the case. What is now needed are concerted efforts to further strengthen local research capacities, and encourage participation in collaborative research and development projects. There are some indications of opportunities for funding such research in the EU’s Horizon 2020 programme and the UNFCC’s Climate Technology Network. Governments in developing countries must focus on the coordination of policies across ministries, thus laying the foundation for the long-term development of a bioeconomy and the multiple options it will offer in the future.