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The Tropical Montane Cloud Forests (TMCF) of South America are ecosystems facing rapid changes due to global warming. Herein, we used species climatic niche models to reconstruct the climatic boundaries of TMCF and to predict range shifts in climate change scenarios. Thirty-two species from three taxonomic groups (plants, birds, and amphibians) were modelled using community-level niche models under current and future climatic scenarios, as determined by two Global Climate Models (GCMs) for the year 2050. The community-level reconstructions were used to detect the overlap of TMCF with surrounding ecosystems and with current protected areas (PA). Approximate 42–54% area reduction and 207–429 m upward elevational shift was predicted under climate scenarios. Accordingly, severe environmental contractions (loss of suitability area) due to climate change were detected by our models. TMCF area within PA may increase 17–38% by 2050. We identified transition zones rather than clear limits of vegetational boundaries of TMCF with adjacent ecosystems, which suggested that both TMCF and transitional zones will be impacted, to what conservation strategies targeting TMCF and adjacent ecosystems should be prioritized.