Abstract Tropical deforestation is mainly driven by agricultural expansion, land grabbing, illegal logging, urbanization, cattle ranching as well as mining. However, extraction of minerals and its impacts in high biodiversity regions are still poorly known, particularly in Colombia, a tropical megadiverse hotspot. Here, using high-resolution datasets of forest cover changes and detailed geospatial mining data for Colombia, we show a growing contribution of legal mining to national deforestation: 3.4% over the 2001–2018 period, with a peak at 5.6% in 2017. During this period, around 121 819 ha have been deforested inside legal mining concessions, and an estimation of over 400 000 ha deforested by both legal and illegal. Gold and coal are the most important legally-mined materials in Colombia associated to deforestation, particularly in the recent years with 511% and 257% tree cover loss increases respectively (average over 2016–2018 compared to 2001–2015 average of mined material deforestation average). Three Colombian departments summed out ∼70% of the national deforestation occurring in legal concessions: in 2018, up to 23% of deforestation in Antioquia was taking place in legal mines (gold producer). Finally, we found that only 1% (respectively, 3%) of the concessions contribute to 60% (>90%) of the legal mining-related deforestation, mainly driven by large clearings to agriculture. Environmental law enforcement, monitoring activities and engaging the mining industry in effective forest conservation and landscape restoration strategies are urgently needed in Colombia for preserving biodiversity and ecosystem services.