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Habitat loss poses a major threat to global biodiversity. Many studies have explored the potential damages of deforestation to animal populations but few have considered trees as thermoregulatory microhabitats or addressed how tree loss might impact the fate of species under climate change. Using a biophysical approach, we explore how tree loss might affect semi-arboreal diurnal ectotherms (lizards) under current and projected climates. We find that tree loss can reduce lizard population growth by curtailing activity time and length of the activity season. Although climate change can generally promote population growth for lizards, deforestation can reverse these positive effects for 66% of simulated populations and further accelerate population declines for another 18%. Our research underscores the mechanistic link between tree availability and population survival and growth, thus advocating for forest conservation and the integration of biophysical modelling and microhabitat diversity into conservation strategies, particularly in the face of climate change.