Industrial mining projects can play an important role in global sustainable development if associated health risks are minimised and opportunities maximised. While a broad body of evidence from quantitative studies exists that establishes the interlinkages between mining operations and effects on public health, little research has been conducted investigating health impacts from the perspective of affected communities. This is particularly true in sub-Saharan Africa, where about a third of the remaining global mineral resources are endowed and health-related indicators for sustainable development are lagging behind. In this multi-country qualitative study, we explore community perceptions regarding impacts of industrial mining on their health and well-being. In nine study sites in Burkina Faso, Mozambique and Tanzania, we conducted 83 participatory focus group discussions with a total of 791 participants (385 men, 406 women). Our findings reveal a broad range of perceived impacts on environmental, economic and social determinants of health, with secondary health implications related to morbidity, mortality and well-being. Overall, perceived negative impacts prevailed, mainly related to environmental pollution, change in livelihoods or social disruption. Perceived positive impacts on health and well-being were related to interventions implemented by the mines such as new or improved water sources, health care facilities, roads and schools. The consistency of these findings across countries and study sites suggests a structural problem and indicates a pressing need to address health by acting on the wider determinants of health in mining regions. Participatory health impact assessment should be strengthened in host countries to foster strategic interventions, include marginalised population groups, and protect and promote the health of local communities. By including community perspectives on health before and during project implementation, policymakers can take advantage of economic opportunities while avoiding the pitfalls, bringing their communities closer to achieving good health and well-being goals by 2030 and beyond.