Abstract
<title>Abstract</title> <p> As climate and land use changes increasingly threaten tropical ecosystems, developing proactive, multi-scalar conservation strategies is vital for endangered megafauna conservation. This study introduces a spatial planning framework to evaluate species distribution, anthropogenic pressures, both land and climate within transboundary landscapes. Using the endangered Borneo pygmy elephant ( <italic>Elephas maximus borneensis</italic> ) as an overlooked flagship case study across a mosaiced landscape spanning Malaysia (Sabah) and Indonesia (North Kalimantan), we built an ensemble model that demonstrated exceptional predictive performance. Over half of the identified critical habitat matrix currently corresponds to active logging and oil palm concessions, driving severe fragmentation over the past decade. By intersecting future climate exposure with localized vegetation quality, we constructed a predictive bivariate conservation planning matrix. Our findings indicate that land-use in non-distribution areas are changing faster than the species distribution areas, with the most extensive losses during 2015–2025 in the forest (23,438.5 ha) and the most significant growth in oil palm (25,204.8 ha). Furthermore, the species distribution within oil palm concessions had experienced significant climate exposure (0.63 ± 0.01). This study suggests that areas with more vegetation and low climate exposure are conservation strategies with potential refugia, mostly located in protected areas of 278,209.21 hectares. We outline targeted, adaptive management interventions required by transnational policymakers, conservation authorities, and corporate concession holders to preserve critical corridors. Besides, this framework provides a reproducible, data-driven approach to reconcile industrial land-use demands with climate-resilient wildlife conservation in complex, cross-border tropical ecoregions. </p>