Because of their steep gradients in abiotic and biotic factors, mountains offer an ideal setting to enhance our understanding of mechanisms that underlie species distributions and community assemblies. We compared the structure of taxonomically and functionally diverse soil fungal communities in soils along elevational gradients in the Neo- and Paleotropics (northern Argentina, Central America, and Borneo). We found that soil fungal community composition reflects environmental factors at both regional and pantropical scales, particularly temperature and soil pH. Elevational turnover is driven by contrasting environmental preferences among functional groups and replacement of species within functional guilds. In addition, we found that habitat preference can already be observed at the level of taxonomic orders, often irrespective of functional guild, which suggests shared physiological constraints and environmental optimum for relatively closely related taxa. Strong biogeographic structure likely reflects dispersal limitation and resulting differences in local species pools of fungi, as well as their hosts or substrates. Although the number of species shared among regions is low, remarkable similarity of functional profiles across regions suggests functional niche proportions may be driven by similar mechanisms across moist tropical forests, resulting in relatively predictable proportions of functional guilds. The pronounced compositional and functional turnover along elevation gradients driven mainly by temperature and correlated environmental factors implies that tropical montane forest fungi will likely be sensitive to climate change, resulting in variation in composition and functionality over time.