Through the study of some architectural details of Choquequirao, which has attributed to Chachapoyan workers the construction of the citadel, it has been possible to deduce that the Inca sovereign responsible for the work was probably Tupac Yupanqui (1471-1493) and it is also possible that was Huayna Capac (1493-1527), as both deported from the conquered lands of the Chachapoyas large numbers of "mitimaes" to work for the benefit of the Inca State.
We presume that the Inca government built Choquequirao for religious and pilgrimage purposes, a sanctuary linked to the tutelary “Apus” (Gods) of this part of the "sierra nevada", without ceasing to suppose that this great work had the purpose of perpetuating the memory of the power of its Ruler builder.
The Incas worshiped nature, and in particular many kinds of natural features such as hills, snow-capped mountains, fountains, rivers, lagoons, which they believed to be alive and full of sacred power. Such supernatural entities were called "Apus".
For the Incas, the action of the wind, the sun and the movement of the water could fill the landscape of divine essence; sites that met these characteristics were preferred to locate shrines and human settlements. Ritual staircases, carved canals, fountains, niches for sacred objects, ceremonial and astronomical observation platforms ("ushnu" in Quechua) are some of the iconic features of the sacred Inca landscape.
Choquequirao contains all the features of these sacred sites.
The Inca administration of Choquequirao, be it political or religious, was gradually ending with the fall of Tahuantinsuyo, beginning perhaps from the fratricidal struggles between Huáscar and Atahuallpa and increasing with the bellicose actions of the Spanish conquest, until the Inca residents were in the extreme situation of not being able to support his servitude.
In the years previous to its abandonment, Choquequirao was always more isolated and its inhabitants had to expand their area of agricultural culture to directly attend their nutritional needs.
About the end of Choquequirao, it is plausible to think that the Chachapoyans who built the citadel, which had ended up being the "yanaconas" (servants) of the incan residents of the complex, rebelled and executed the Inca proxies, running away successively from the place.
As a result of its abandonment Choquequirao was soon claimed by the jungle, who hid the Sanctuary under its protective vegetal mantle.