Documentation of paleoclimatic conditions during the last glacial stage in the tropical Andes is sparse despite the importance of understanding past climate changes in the tropics. To reconstruct paleoenvironmental conditions in the alpine neotropics, we measured the oxygen (δ18O) and hydrogen (δD) isotopic composition of authigenic kaolinite within weathering profiles of the Bogota basin (Colombia) because of the strong dependence of isotopic values on both surface temperature and rainfall. While kaolinite isotope data from Holocene soils in the basin reflect modern mean annual temperature and mean weighted rainwater isotopic composition of the basin, kaolinite isotope data from paleosols developed during the last glacial stage suggest 6 ± 2 °C cooler temperatures. Moreover, the isotope data indicate higher isotopic values of paleorainwater, interpreted to reflect drier conditions. The combination of reduced rainfall, temperature, and pCO2 significantly affected the distribution of tropical montane flora during the last glacial stage.