The Colca Canyon has been inhabited for more than 1,500 years, originally by pre-Inca ethnic peoples, who developed a complex agricultural system of Andean terraces along the valley.  In the past the terraces covered more than 10,000 hectares of the Colca Canyon and today large sections of the Andean terraces remain and are still cultivated by the local people. Indeed the cabins of the Incas are still used by locals to house crops to this day.

Remains of the original Inca settlements can be seen dotted throughout the Colca Canyon.  In Spanish & Colonial times the Collaguas and the Cabanas built towns and churches along the Canyon after the Viceroy, Toledo ordered that the Indian population of the valley be gathered in 14 villages. 
 
Evidence of the towns of this time remains and one of the oldest churches in Peru, the Santiago Apostol, built in 1569 can be seen at Coporaque. 

In the 1980's the Majes Irrigation Project was set up to divert water from the Colca River to the Majes agricultural region. As part of the project a road into the area was built and from then entry to the Colca Canyon for visitors became easier.