The Yanomami, an Indigenous people from the Amazon, confront multifaceted challenges endangering their health and cultural integrity. Of immediate concern is the surge in malaria cases in their territory during Bolsonaro’s government. We investigated the impact of land use on malaria incidence among the Yanomami leveraging satellite imagery and ran difference-in-differences analyses to ask whether the Yanomami suffered disproportionately from malaria when illegal mining was rising in the region (2016-2022). We show a remarkable ~300% rise in malaria from 2016 to 2022 and point to mining as the primary driver of malaria among the Yanomami; when mining increases by 1%, malaria increases by 31%. After mining unfolded, the burden of malaria among the Yanomami was disproportionately higher, up to 15%, than in non-indigenous communities. Our findings underscore the impact of illegal mining on the high malaria burden suffered by the Yanomami and the importance of rainforest conservation and land sovereignty for Indigenous health.