From The Penguin History Of Latin America, by Edwin Williamson (Penguin, 2003), Kindle pp. 85-87:
In the course of the Spanish Conquest and the decades immediately following it, the imperial structures of the Aztecs and the Incas were destroyed, their royal families and imperial nobility deprived of their power. It was this native ruling aristocracy which had most reason to lament the passing of the old order, and the expressions of their nostalgia and sorrow have come down to us in writings which have all too often been taken as representative of the generality of Indians.
Once the Spaniards had got the upper hand, the Indian aristocracy faced the choice of either collaborating with their conquerors or organizing rebellions in order to recover their former power. As we have seen, the young prince Manco Inca in Peru at first chose collaboration in the hope of outmanœuvring dynastic rivals for the imperial title, but later decided to rebel against the Spaniards once he realized that the conquistadors had no intention of quitting the country. Even in later generations it was possible for aristocratic collaborators to change their minds and attempt to rebel against Spanish power. This type of resistance was élitist and dynastic, having little to do with the defence of the mass of Indians. But dispossession was not, in fact, the fate of the Aztec and Inca nobles; so long as they accepted Spanish sovereignty, they were allowed to retain their aristocratic status in post-Conquest society: they were awarded lands and encomiendas by the Spanish monarch, and their children were educated in schools for nobles, such as the college at Tlatelolco in Mexico and those of Huancayo and Cuzco in Peru.
There were Indian kingdoms which actually formed alliances with the Spanish invaders against their historic enemies. In Mexico the most famous example is that of the Tlaxcalans, who attacked Tenochtitlán and helped Cortés raze the city to the ground; in Peru the support of the Huanca people was crucial to Pizarro’s defeat of the Incas. ‘Such alliances expressed the internal contradictions and discontents that plagued Aztec and Inca rule, and the failure of these empires to eradicate the independent military potential of resentful ethnic kingdoms.’ Even after the Spanish Conquest had been completed, numerous ethnic kingdoms and tribes decided to collaborate with the new masters in order to seek advantage against rivals, regain lost territory or rid themselves of domination by hated enemies. The crumbling of the pre-Hispanic empires had the effect, therefore, of devolving identity and autonomy to subjugated ethnic kingdoms, and of revitalizing the authority of ethnic chieftains. It was this class of chiefs, called pipiltin in Mexico and curacas in Peru, that dealt with the Spaniards and organized their own people to offer tribute and labour services to the Spanish encomenderos.
Within these Indian kingdoms and communities, traditional life went on much as before, and, having accepted the new masters, it made sense also to accept their religion. Even so, relations with the Spaniards were unstable in the aftermath of the Conquest. If a kingdom or tribe came to believe that its interests were no longer being served by alliance with the Spaniards, it might attempt to resist them or even rebel. In Peru during the 1560s the most radical of these rebellions was that of the millenarian movement called Taki Onqoy in the region of Huamanga, where many tribes previously loyal to the Spaniards turned against them in reaction to excessive labour demands, and called for the outright rejection of Spanish law and religion, appealing to their gods to help them expel the invaders.
Yet even though the basic structures of Indian life at the communal and tribal levels remained largely unchanged by the Conquest, none the less many villages, crops and individual lives were destroyed in the course of the wars (in Peru, it must be remembered, a bitter civil war had been raging for several years before the Spaniards arrived). There is no doubt that large numbers of Indians suffered torture and rape at the hands of the conquistadors. Labour for the encomenderos must often, though not always, have been harsh and exploitative, since many Spaniards were not interested in settling down but simply wanted to extract as much wealth as possible from the Indies before returning to Spain. The Conquest also disrupted communities; many Indians took to wandering the countryside as vagabonds or fled the Spaniards to hide in the wilderness. This kind of dislocation was particularly common in Peru, where the mitmaq system, based on ‘vertical archipelagos’ or outlying colonies, partially broke down, leaving many colonists cut off from their tribal homelands. One option for such displaced individuals was to enter the service of Spaniards as part of that class of commoner called naborías in Mexico and yanaconas in Peru – detribalized Indians who used to serve as personal retainers to the Aztec and Inca aristocracies and whom the Spaniards also employed.