In 1471, the Inca Tupac Yupanqui conquered the north part of Chile all the way to the Bio Bio River, as well as the high plateau of Bolivia and the northeastern part of Argentina.  This way San Pedro de Atacama became a part of Collasuyo, one od the four paths that formed part of the Inca empire (Tiwantisuyo) ... 

Tupac Yupanqui organized the empire and distributed the land to the "mitimaes" (families that were forced to migrate to this area to exert order and to manage the rebelious villages). 

The Incas established alliances with the Atacamanean Leaders, and their managing centers were set outside the Atacamanean villages. This way both cultures were able to live together in peace. They established managing centers in Catarpe, and they settled in Turi, Calama, Río Grande, Chiu Chiu, among other villages.

The Inca empire imposed new religious beliefs such as, the cult (worship)to the Sun, emphasizing the sanctuary at the summit of the Licancabur volcano, making the quechua language official.   They also imposed the Ayllo system, communities formed by related familiess who worked the land as a cooporative

In 1536, after 70 years, the Inca empire was conquered by the Spaniards, thus putting an end to the prehispanic empire, and bringing about great  social , economic, and political changes. The Inca culture was unable to impose itself over the solid Atacamanean culture, however it did exert influence over the ceramic, textile, and on high summit cult practices.