Siege of Cuzco The Siege of Cuzco was the May 6 , 1536 – March 1537 , ten - month siege of the city of Cuzco by the army of Inca Emperor Manco Inca Yupanqui against a garrison of Spanish conquistador s and Indian auxiliaries led by Hernando Pizarro . A Spaniard expedition led by Francisco Pizarro had captured the Inca capital of Cuzco on November 15 , 1533 after defeating an Inca army headed by general Quisquis . The following month , the conquistador s supported the coronation as Inca emperor of Manco Inca to facilitate their control over the empire . However , real power rested with the Spaniards who frequently humiliated Manco Inca and imprisoned him after an attempted escape in November 1535 . After his release in January 1536 , Manco Inca managed to leave Cuzco on April 18 promising the Spanish commander , Hernando Pizarro , to bring back a large gold statue when in fact he was already preparing a rebellion . Having realized their mistake , Hernando Pizarro led an expedition against Manco Inca ' s troops , which had gathered in the nearby Yucay Valley , however , the attack failed as the Spaniards had severely underestimated the size of the Inca army . The Inca emperor did not attack Cuzco at once , instead he waited to assemble his full army estimated at between 100 , 000 to 200 , 000 men strong around the city ( some sources suggest numbers as low as 40 , 000 ) ; against them there were 190 Spaniards , 80 of them horsemen , and several thousand Indian auxiliaries . The siege started on May 6 , 1536 with a full - scale attack towards the main square of the city ; the Inca army succeeded in capturing most of the city while the Spaniards took refuge in two large buildings near the main plaza . The conquistadors managed to fend off Inca attacks from these constructions and mounted frequent raids against their besiegers . To relieve their position , the Spaniards decided to assault the walled complex of Sacsayhuamán , which served as the main base of operations for the Inca army . Fifty horsemen , led by Juan Pizarro , and accompanied by Indian auxiliaries broke through the Inca army files , turned around and attacked Sacsayhuamán from outside the city . During the frontal assault against the building ' s large walls , a stone struck Juan Pizarro in the head ; he died days later from the injury sustained . The following day , the Spaniards resisted several Inca counterattacks and mounted a renewed assault at night using scaling ladders . In this way , they managed to capture the terrace walls of Sacsayhuamán while the Inca army held on to the two tall towers of the complex . The Inca commanders , Paucar Huaman and the high priest or Villac Umu , decided to leave the confinement of the towers and fight their way towards Calca , the site of Manco Inca ' s headquarters , to bring back reinforcements . The attempt was successful and the towers were left under the command of Titu Cusi Gualpa , an Inca nobleman . However , despite Titu ' s fierce resistance , the Spaniards and their auxiliaries managed to storm the towers so that when the Inca commanders returned , Sacsayhuamán was firmly under their control . The capture of Sacsayhuamán eased the pressure on the Spanish garrison at Cuzco ; the fighting now turned in a series of daily skirmishes interrupted only by the Inca religious tradition of halting attacks during the new moon . During this period , the Spaniards successfully implemented terror tactics to demoralize the Inca army , which included an order to kill any woman caught and cutting off the hands of captured men . Encouraged by their successes , Hernando Pizarro led an attack against Manco Inca ' s headquarters which were now at Ollantaytambo , further away from Cuzco . However , Manco Inca managed to defeat the Spanish expedition at the Battle of Ollantaytambo by taking advantage of the fortifications and the difficult terrain around the site . The Spanish garrison had more success with several raids to gather food from regions near Cuzco ; these incursions allowed them to replenish their almost exhausted provisions . Meanwhile , Manco Inca tried to capitalize on his success at Ollantaytambo with a renewed assault on Cuzco ; however , a Spanish cavalry party had a chance encounter with the Inca army thus ruining any hope of surprise . That same night the Spaniards mounted a full scale attack which achieved complete surprise and inflicted severe casualties on Manco Inca ' s troops . After 10 months of vicious fighting in Cuzco , with low morale playing a factor , Manco Inca decided to raise the siege at Cuzco and withdraw to Vilcabamba . It is suggested by some that by this action he threw away his only real chance to rebuff the Spaniards from Tawantinsuyu ; however , it was probably the only realistic choice he had considering the arrival of Spanish reinforcements from Chile led by Diego de Almagro . Upon facing victory and the availability of expanding his own reign into Peru , Almagro seized the city once having achieved victory for Spain and had Hernando and Gonzalo imprisoned . Gonzalo managed to escape , however , to later face Almagro in a personal triumph at the battle of Las Salinas .