Scientific studies concerning the causes and consequences of the biodeterioration of stone monuments located at high altitudes in permanently cold, mountainous regions are scarce. For that reason, this study aimed to detect and identify the bacteria involved in the deterioration of this type of monument. To achieve this goal, we focused on the most important archeological Inca site in the Ecuadorian Andes: Ingapirca’s Temple of the Sun, built approximately 500 years ago at 3.100 m.a.s.l. We first examined the stone surfaces of the temple by scanning electron microscopy and showed the detrimental impact on the mineral structure of the green andesite mineral used to build the temple, caused by crustose lichen thalli and heterotrophic bacteria. Then, we isolated, characterized, and identified several of these bacteria. Most of them multiplied at a wide range of temperatures, from 4 °C to 30 °C, and were thus considered eurypsychrophiles. Actinobacteria and Proteobacteria species dominated the culturable fraction of this community. Several isolates produced metabolites that solubilized mineral phosphates at low temperatures; others solubilized iron-containing mineral fractions in the green andesite rock when tested in vitro. To the best of our knowledge, this is the first report related to the biodeterioration of an Inca monument at such an altitude in the Andes range.