The inspiration for the church's creation was a purported miraculous event in 1576 (maybe), when amerindian Maria Meneses de Quiñones and her deaf-mute daughter Rosa were caught in a very strong storm. The two sought refuge between the small Lajas (slabs of stone), when, to Meneses' surprise, her daughter Rosa exclaimed "the Mestiza is calling me" and pointed to a lightning-illuminated silhouette over the laja. This apparition of the Virgin Mary instigated popular pilgrimage to the site and occasional reports of cases of miraculous healing. An image appeared in the stone that is several feet inside of it. The image in the stone is still visible today.[1]

The existence of a shrine in this location was recorded in the accounts of friar Juan de Santa Gertrudis' journey through the southern region of the New Kingdom of Granada between 1756 and 1764. The first shrine was built here in the middle of 18th century from straw and wood. It was replaced with a 7 meter long brick chapel in 1795/96. From 1802 on, a new, larger shrine was built, which in turn was extended and connected to the opposite side of canyon with a bridge in the second half of the 19th century.

The current church was built between January 1, 1916, and August 20, 1949, with donations from local churchgoers. It rises 100 m (330 ft) high from the bottom of the canyon and is connected to the opposite side of the canyon by a 50 m (160 ft) tall bridge.[2]

The shrine is located in southern Colombia and has been a tourism and pilgrimage destination since the eighteenth century. The Spanish Franciscan Juan de Santa Gertrudis (1724–1799) mentions the sanctuary in Book III, Part 2, of his four-volume chronicle of his 1756–62 journey in the south portion of the Kingdom of New Granada (titled "Wonders of Nature"). This is possibly the oldest reference to its existence.