Large private sector investments in low- and middle-income countries are often critically evaluated with regards to their environmental, social, human rights, and health impacts. A health impact assessment, including a baseline health survey, was commissioned by the Addax Bioenergy Sierra Leone project in 2010. As part of the monitoring, a follow-up survey was conducted three years later. A set of health indicators was assessed at six impacted and two control sites. Most of these indices improved, particularly at the impacted sites. The prevalences of stunting, wasting, and Plasmodium falciparum in children under five years of age decreased significantly at impacted sites (all p < 0.05) and non-significantly at control sites. Anemia in children and in women of reproductive age (15–49 years) decreased significantly at impacted and control sites (p < 0.05 and p < 0.001, respectively). Health facility-based deliveries increased significantly at the impacted sites (p < 0.05). The prevalences of helminth infections in children aged 10–15 years remained approximately at the same levels, although focal increases at the impacted sites were noted. Access to improved sanitation decreased significantly (p < 0.05) at control and non-significantly at impacted sites. Water quality remained poor without significant changes. The epidemiologic monitoring of a bioenergy project provides a useful contribution for evidence-based decision-making.