 In 1531 , a group of Spaniards led by Francisco Pizarro landed on the shores of the Inca Empire , thus starting the Spanish conquest of Peru . At that time the empire was emerging from a civil war in which Atahualpa had defeated his brother Huascar to claim the title of Sapa Inca . Atahualpa underestimated the strength of the small force of Spaniards and was captured during an ambush at Cajamarca in November 1532 . Pizarro ordered the execution of the emperor in July 1533 , and occupied the Inca capital of Cusco four months later . To replace Atahualpa , Pizarro installed his brother Túpac Huallpa as a puppet ruler , but he died shortly afterwards . Another brother , Manco Inca , was crowned in his place . During this stage , Atahualpa 's generals were the only opposition to the Spanish advance as a sizable part of the empire 's population had fought on Huascar 's side during the civil war and joined Pizarro against their enemies . 
