Energy supply and accessibility has a major impact on the development of societies. Modern bioenergy production in the form of heat, electricity, and liquid transportation fuels is increasingly cost competitive as prices of fossil fuels continue to increase. However, the large potential benefits associated with bioenergy come with a price tag and risks that may be disproportionately carried by tropical and non-industrialized countries. This analysis focuses on the influence of project scale on economic, social, and environmental impacts of bioenergy production in the tropics using the framework of two wood fueled bioenergy projects in Uganda—a large (50 MW) and a small-scale (200 kW). There are indications that less sustainable practices often come with increasing project-scale. This study found that a distributed, small-scale infrastructure indeed can be more desirable in terms of resource efficiency, impacts on ecosystems and local societies, and financial risks and benefits compared with those associated with one large-scale. To support the implementation of small-scale projects, there is a need for policies fostering distributed energy infrastructure and participatory tools beyond traditional cost-benefit analysis to assess sustainability of bioenergy systems.