The museum showcases ethnographic materials collected by Capuchin missionaries in the mid- to late-19th century in the vast Andean-Amazonian region of Colombia, which is irrigated by the Caquetá, Putumayo and Amazon rivers and stretches from the foothills of the Andes to the border between Colombia, Brazil and Peru.

The collection in the Museu Etnogràfic Andino - Amazònic includes important examples of ethnographic materials and zoological and botanical specimens from the Andes and Amazon, as well as pre-Columbian ceramics, indigenous crafts, ritual masks and other objects that bear witness to other cultures.