After the successful Spanish conquest of the Inca Empire, the assassination of Francisco Pizarro in 1541, and the execution of his main antagonist, Diego de Almagro (1538) and his son, El Mozo (1542), most of the competent commanders of the recently founded New Castile Governorate had been lost in the ensuing power struggle.

With his namesake as an ensuring symbol of the former reign of the Pizarros, he gathered supporters, mainly opposed by formal governor of New Castile, Cristóbal Vaca de Castro, victor at Chupas over the Almagristas.

The two gathered supporters and met on January 18, 1546 at Añaquito in present-day Ecuador, superiority in numbers and firepower ensured victory for Gonzalo Pizarro, who crushed the army of Blasco Núñez Vela, who was decapitated on the field of battle.

The king then appointed Pedro de la Gasca as new governor of Peru; meanwhile, the land itself fell under control by Gonzalo Pizarro and his forces.

De la Gasca landed in Peru in 1547, winning supporters to his initially inferior forces by promising amnesty to those having committed treason to the crown, and proclaimed he would not enforce the New Laws, whose dispositions demanding better conditions for native laborers had led many powerful encomenderos to join Pizarro's cause.