Artisanal and small-scale mining (ASM) provides a vitally important livelihood for millions of people in many low- and middle-income countries. ASM can result in habitat clearance, increased hunting pressure, pollution, and sedimentation of waterways. Consequently, where mineral and biological wealth coincide, there are trade-offs. Here, we combine geological data with four datasets capturing conservation priorities, to evaluate where, and to what extent, mining may impact biodiversity, and to explore opportunities for both to co-exist. We use Madagascar as a case study: a biodiversity hotspot rich in economically important minerals where artisanal gem mining has conflicted with biodiversity conservation. We identify areas of Madagascar most likely to host primary deposits of gems and find that 11% - 14% of the most important area for biodiversity on the island could host primary gem deposits. However, we also identify 7 million hectares (80%) of potentially prospective land which is outside of these areas. Establishing decentralised, community-managed zones for licensed ASM in such areas could help to incentivise formalisation and minimise social and environmental trade-offs. Our mapping approach could be applied in other countries to encourage the establishment of designated zones for ASM in places where mining does not conflict with conservation.