Our research endeavors to evaluate the precise ramifications of climate change on Iran’s protected regions, utilizing species distribution modeling to anticipate the effects of climate change on 394 bird species, 157 plant species, 72 reptiles, and 20 mammals across two climate change scenarios: SSP245 and SSP585 in 2070. Subsequently, we employed binary species distribution maps to determine the extent of overlap between 125 protected areas, 27 wildlife refuges, and 15 national parks and species distribution, quantifying the proportion of these areas encompassed by their distribution. We found that under the SSP585 scenario, 174 bird species could experience a 319% expansion in suitable habitats, while 220 species could decline by 57.1%. Among plants, 16 species are projected to grow by 40.3%, whereas 141 species may decrease by 68.8%. Reptiles could experience an increase of 279.1% in 24 species, with a 66.6% decrease in 48 species, while mammals may witness a significant increase of 147.3% in 5 species, but a 71.8% decrease in 15 species. Also, under the SSP585 scenario, in national parks, bird coverage declines from 32.2% (current) to 19.9%, plants from 24.2 to 13.2%, reptiles from 18.4 to 6.8%, and mammals from 17.7 to 10%. In wildlife refuges, birds decrease from 9.7 to 5.7%, plants from 10.9 to 4.6%, reptiles from 12.9 to 2.5%, and mammals from 7.4 to 4.3%. In protected areas, birds drop from 29.3 to 20.4%, plants from 27.7 to 12.5%, reptiles from 18.7 to 9.7%, and mammals from 24 to 12.1%. The low overlap of species with national parks, wildlife refuges, and protected areas underscores the importance of re-evaluating and potentially expanding protected areas to ensure they encompass a broader range of habitats, particularly those that are underrepresented, to enhance the conservation of Iran’s biodiversity amidst the challenges posed by climate change.