The uplift of mountain areas allows the creation of new ecological spaces, promoting adaptive radiation. Empirical evidence shows that the Andean uplift has driven species diversification, with multiple biogeographic movements from lowlands to highlands and vice versa over the last 15 million years in plant and animal clades. However, the relationship between the evolution of phenotypic traits, particularly climate niches, and biogeographic transitions across elevational gradients is still poorly understood. Specifically, it is unknown how different lineages evolved to tolerate colder temperatures as they colonized highlands throughout their evolutionary history. Here, we test whether biogeographic transitions between lowlands and highlands in South America are associated with evolutionary shifts in climate niche traits for South American squamates. Using a combination of spatial and phylogenetic comparative methods, we found higher evolutionary rates for annual mean and minimum temperatures for mountain species relative to lowland lineages. By contrast, we did not find differences in maximum temperatures for species in lowland and highland areas. We also found that transitions from lowlands to mountains were highly recurrent, although dispersal toward lowlands was more frequent than mountain colonization. Our results suggest that lizards and snakes have repeatedly evolved to tolerate colder environments as they moved into highland areas, likely due to evolutionary flexibility in traits related to cold tolerance, in contrast to strong conservatism in traits related to heat tolerance.