The high biodiversity of the Mexican montane forests is concentrated on the Trans‐Mexican Volcanic Belt, where several Protected Natural Areas exist. Our study examines the projected changes in suitable climatic habitat for five conifer species that dominate these forests. The species are distributed sequentially in overlapping altitudinal bands: Pinus hartwegii at the upper timberline, followed by Abies religiosa, the overwintering host of the Monarch butterfly at the Monarch Butterfly Biosphere Reserve, P. pseudostrobus, the most important in economic terms, and P. devoniana and P. oocarpa, which are important for resin production and occupy low altitudes where montane conifers merge with tropical dry forests. We fit a bioclimatic model to presence–absence observations for each species using the Random Forests classification tree with ground plot data. The models are driven by normal climatic variables from 1961 to 1990, which represents the reference period for climate‐induced vegetation changes. Climate data from an ensemble of 17 general circulation models were run through the classification tree to project current distributions under climates described by the RCP 6.0 watts/m2 scenario for the decades centered on years 2030, 2060 and 2090. The results suggest that, by 2060, the climate niche of each species will occur at elevations that are between 300 to 500 m higher than at present. By 2060, habitat loss could amount to 46–77%, mostly affecting the lower limits of distribution. The two species at the highest elevation, P. hartwegii and A. religiosa, would suffer the greatest losses while, at the lower elevations, P. oocarpa would gain the most niche space. Our results suggest that conifers will require human assistance to migrate altitudinally upward in order to recouple populations with the climates to which they are adapted. Traditional in situ conservation measures are likely to be equivalent to inaction and will therefore be incapable of maintaining current forest compositions.