The effect of climate change on the ecological niche of species represents one of the main threats in maintaining processes and functions in mountain ecosystems. However, these links have rarely been assessed due to the lack of application of ecological niche models at the species assemblage level. Therefore, in this study we integrated species ecological niche modeling techniques to predict assemblage changes in tropical montane systems. We estimate species richness and functional diversity for 2040 and 2060, based on the modeled niche of 39 native tree-shrub-herbaceous species of the montane of Mexico, using a model selection protocol for Maxent and Minimal Volume Ellipsoid (MVE) models in which we selected models based on the statistical significance of the partial ROC test, low omission rates, values of the area under the curve, and the Akaike Information Criterion. We project functional diversity, considering nine functional traits related to primary productivity, rate of decomposition, and natural regeneration. Our results show a high loss rate of species richness and functional diversity at low elevations (1500-2800 m a.s.l.). At high altitudes (2800-3500 m a.s.l.), we find a greater richness of species, without increases in functional diversity. We find that tree species are more likely to maintain their current geographic distribution ranges, while herbaceous species show a large loss of species richness at low and mid-elevations. Therefore, we provide evidence that the effects of climate change will promote imbalances in species assemblage and probably cause a loss of processes and functions, such as soil decomposition and soil organic matter, mainly in low-elevation areas.