Later, when he heard the rumours about the wealth of the Inca Empire, he joined forces with Francisco Pizarro in two failed expeditions of conquest. With a royal authorization obtained a year earlier, in 1530 Francisco Pizarro undertook a new expedition alone that would lead him, after skillfully taking advantage of the disagreements between the Inca sovereign Atahualpa and his half-brother Huáscar, to the conquest of the Inca Empire. From then on, Almagro dedicated himself to the exploration of the southern territories of the Inca Empire, in present-day Chile, up to the Aconcagua Valley. In 1535, Emperor Charles V rewarded him with the governorship of Nueva Toledo, in southern Peru, and the title of advance in the
lands beyond Lake Titicaca.
Upon his return to Peru in 1537, Almagro occupied the city of Cuzco, considering it to belong to his governorship. This fact led to a bloody confrontation between Almagro and slate workers that ended with the victory of the Pizarro brothers in the battle of the Salinas, in April 1538. Made prisoner, Almagro was executed in July of that year.