As habitat destruction intensifies due to expanding human infrastructure, balancing biodiversity conservation with resource extraction has become a global challenge. Thus, quantifying the extent and location of proposed mining operations is key to mitigating the impacts on threatened species. This issue is particularly acute in the biodiversity hotspots of southeast Asia, where rapid economic growth needs to be balanced with sustainable conservation management of the remaining tropical forest. The Philippine Eagle (Pithecophaga jefferyi), a critically endangered tropical forest raptor endemic to the Philippines, faces increasing threats from mining activities that destroy and fragment its tropical forest habitat. Here, we integrate Species Distribution Modelling with gap and hotspot analysis to assess the spatial overlap between Philippine Eagle nest habitat and mining concessions across a protected area network on Mindanao, where the largest population remains. Using a landscape-scale SDM built with remote sensing covariates and eagle occurrence data, we identified high-suitability nest habitats and projected these into the Eastern Mindanao Biodiversity Corridor (EMBC). Hotspot analysis revealed that 41 % of the total mining concessions area contained high-suitability nest habitat, highlighting significant conservation risks. Additionally, 46 % of indigenous ancestral domains contain high-suitability nest habitat, emphasizing the importance of indigenous land management in safeguarding eagle habitats. Our gap analysis demonstrated that 35 % of the EMBC protects high-suitability nest habitat, which here represents the remaining montane tropical forest. To mitigate mining impacts, we propose targeted nest surveys in high-risk areas, implementation of mining moratoriums near critical nesting zones, and strengthening indigenous and protected area land management. By integrating SDMs with spatial analysis, we provide a framework for directing conservation efforts to balance resource extraction with the preservation of the Philippine Eagles habitat. Our findings offer crucial insights for policy development and land-use planning to protect this iconic species and its threatened habitat.