With Atahualpa dead, the Spaniards proceeded to march on Cusco. On the way, they dealt another decisive blow, aided by native American allies from the pro-Huáscar faction, to the still formidable remnants of Atahualpa's army. Then on November 15, 1533, exactly a year after arriving at Cajamarca, Pizarro, reinforced with an army of 5,000 native American auxiliaries, captured the imperial city and placed Manco Cápac II, kin of Huáscar and his faction, on the Inca throne as a Spanish puppet.

Further consolidation of Spanish power in Peru, however, was slowed during the next few years by both indigenous resistance and internal divisions among the victorious Spaniards. The native population, even those who had allied initially with the invaders against the Incas, had second thoughts about the arrival of the newcomers. They originally believed that the Spaniards simply represented one more in a long line of Andean power-contenders with whom to ally or accommodate. The continuing violent and rapacious behavior of many Spaniards, however, as well as the harsh overall effects of the new colonial order, caused many to alter this assessment. This change led Manco Cápac II to balk at his subservient role as a Spanish puppet and to rise in rebellion in 1536. Ultimately unable to defeat the Spaniards, Manco retreated to Vilcabamba in the remote Andean interior where he established an independent Inca kingdom, replete with a miniature royal court, that held out until 1572.

Native American resistance took another form during the 1560s with the millenarian religious revival in Huamanga known as Taki Onqoy (literally "dancing sickness"), which preached the total rejection of Spanish religion and customs. Converts to the sect expressed their conversion and spiritual rebirth by a sudden seizure in which they would shake and dance uncontrollably, often falling and writhing on the ground. The leaders of Taki Onqoy claimed that they were messengers from the native gods and preached that a pan-Andean alliance of native gods would destroy the Christians by unleashing disease and other calamities against them. An adherent to the sect declared at an official inquiry in 1564 that "the world has turned about, and this time God and the Spaniards [will be] defeated and all the Spaniards killed and their cities drowned and the sea will rise and overwhelm them, so that there will remain no memory of them."

To further complicate matters for the conquerors, a fierce dispute broke out among the followers of Pizarro and those of Diego de Almagro. Having fallen out over the original division of spoils at Cajamarca, Almagro and his followers challenged Pizarro's control of Cusco after returning from an abortive conquest expedition to Chile in 1537. Captured by Pizarro's forces at the Battle of Salinas in 1538, Almagro was executed, but his supporters, who continued to plot under his son, Diego, gained a measure of revenge by assassinating Pizarro in 1541.

As the civil turmoil continued, the Spanish crown intervened to try to bring the dispute to an end, but in the process touched off a dangerous revolt amongc73 ng the colonists by decreeing the end of the encomienda system (see Glossary) in 1542. The encomienda was a much abused prerogative to extract labor and tribute from the indigenous peoples in return for the responsibility to protect and Christianize them. It had originally been granted as a reward to the conquistadors and their families during the conquest and ensuing colonization, and was regarded as sacrosanct by the grantees, or encomenderos, who numbered about 500 out of a total Spanish population of 2,000 in 1536. However, to the crown it raised the specter of a potentially privileged, neofeudal elite emerging in the Andes to challenge crown authority.

The crown's efforts to enforce the New Laws (Nuevos Leyes) of 1542 alienated the colonists, who rallied around the figure of Gonzalo Pizarro, the late Francisco's brother. Gonzalo managed to kill the intemperate Viceroy Don Blasco Núñez de la Vela, who, on his arrival, had foolishly tried to enforce the New Laws. In 1544 Pizarro assumed de facto authority over Peru. His arbitrary and brutal rule, however, caused opposition among the colonists, so that when another royal representative, Pedro de la Gasca, arrived in Peru to restore crown authority, he succeeded in organizing a pro-royalist force that defeated and executed Pizarro in 1548. With Gonzalo's death, the crown finally succeeded, despite subsequent intermittent revolts, in ending the civil war and exerting crown control over Spanish Peru.

It would take another two decades, however, to finally quell native American resistance. Sensing the danger of the Taki Onqoy heresy, the Spanish authorities moved quickly and energetically, through a church-sponsored anti-idolatry campaign, to suppress it before it had a chance to spread. Its leaders were seized, beaten, fined, or expelled from their communities. At the same time, a new campaign was mounted against the last Inca holdout at Vilcabamba, which was finally captured in 1572. With it, the last reigning Inca, Túpac Amaru, was tried and beheaded by the Spaniards in a public ceremony in Cusco, thereby putting an end to the events of the conquest that had begun so dramatically four decades earlier at Cajamarca.

Data as of September 1992