The Andean region in Colombia is heavily populated and has suffered significant habitat conversion and loss, which leads to declining amphibian species richness and abundance. The Colombian Andes encompass a complex array of ecosystems, from tropical rainforests to alpine habitats, and comprise four distinctive life regions with different elevations: Tropical (100–1000 m); sub-Andean (1000–2350 m); Andean (2350–3500 m); and Paramo region (>3500 m). Here we aim to answer: (1) What are the differences in species richness and beta diversity and the number of threatened species across the four life regions? (2) How do human impacts affect each life region and threatened species? We found that the nestedness component dominated taxonomic beta-diversity overall, with differences across the life regions. Further, the percentage of threatened species was higher at higher elevations, with the percentage of threatened species being 30% in the Tropical region and ranging between 55% and 66% at higher elevations. The increase with elevation was also true for human density and proportion of pasture within species range area. Our study offers new insights into biodiversity patterns at regional levels and could inform conservation planning with regard to the optimal spatial arrangement of conservation areas.