The shrine was constructed at the foot of a small, steep, hill in a location formerly known as the Temple of the Sun – an area sacred to the Inca – it remains as one of two principle sacred places to both the indigenous peoples and Catholics alike; the other location being the Virgin of Urkupiña near Cochabamba, Bolivia.

[4][5] In 1589, friars of the Order of Saint Augustine were entrusted with the management of the shrine, establishing a monastery and maintaining a detailed record of the Virgin's miracles.

The current building was built between 1669 and 1679[7] by the Spanish architect Francisco Jiménez de Siguenza replacing the former church.

[3] The hilltop overlooking Lake Titicaca was rededicated as a "calvario" or replica of Calvary and is topped by the Stations of the Seven Sorrows of Mary and an altar with a depiction of the crucifixion of Jesus.

[8] Initial reports indicate that twenty-eight items, including the sculpture of the baby Jesus, were removed from the Virgen de Copacabana by thieves who entered the building using a ladder stolen from a nearby telecommunications station.