After the murder of Atahualpa Huascar’s relatives would join Francisco Pizarro along with thousands of ethnic men opposed to the Incas, so Pizarro was honored in Cusco and the city was occupied without a battle, then the conquistador founded the city from Lima. Shortly after, the civil war between the conquerors was provoked by the repartimiento of the encomiendas of the new territory. In 1542, the Viceroyalty of Peru was established, which initially covered de jure a geographic space from what is now Panama to the southern tip of the continent.
The new order provoked a new uprising known as the encomenderos rebellion. In the 1570s, Viceroy Francisco de Toledo reorganized the territory by pacifying the country from internal wars and culminating with the Inca resistance. Peru a profound social and economic transformation. A mercantilist system was established, supported by the mining of gold and silver, mainly from Potosí, the commercial monopoly and the exploitation of indigenous labor under forced labor or mita.
From the late seventeenth and early eighteenth centuries, the collection of the Crown was slowly undermined by the decline of mining and the consequent economic diversification, as well as commercial smuggling. In this context, the Bourbon reforms were imposed, which subtracted political power from the Lima elite and economically affected internal trade, which produced various uprisings of which the one with the greatest repercussion was the rebellion of the descendant of the Incas Tupac Amaru II; the latter came to endanger the viceregal government in Cusco, but by taking racial overtones against criollos indiscriminately, it precipitated its defeat.
After the death of Túpac Amaru, the indigenous culture was strongly repressed by the Bourbon authorities and delayed the emancipatory projects given the fear of new assonations against the peninsular and creole elite. There is no doubt that Cusco was the main city of all the Tahuantinsuyo, when the Spaniards took it, the Inca resistance significantly diminished, not only because the whole organization of the empire was there, but also because of the meaning it had for the Inca armies. see their capital taken and dominated by the Spaniards.
There are many other rooms and greatness in this city; they pass on both sides two rivers that are born a league above Cusco, and from there until they reach the city and two leagues below, all are paved so that the water runs clean and clear and although it grows it does not overflow; they have their bridges so they enter the city …
In the eighteenth century, several indigenous uprisings took place in reaction to the abuses of the Spanish corregidores, the lack of justice, the delay in claims, and the undue collection of taxes, which include such figures as Juan Santos Atahualpa, Túpac Amaru II and Tupac Katari. The rebellion of Túpac Amaru II was the most social and political uprising of this era. On November 4, 1780, Tupac Amaru II managed to prepare a revolutionary movement that endangered the power of the monarchy. That night he took the prisoner Antonio Arriaga prisoner, who forced him to hand over the royal funds and then ordered him to be executed as punishment for his cruelties.
Later, he managed to organize a considerable army of natives; In Cuzco the corregidores nearby met and also organized an army that left in the search for Túpac Amaru. Both armies met in the town of Sangarará, a brutal and bloody battle being fought out of which Túpac Amaru II emerged victorious. In Cusco, on May 18, 1781, he was put on trial and condemned to die along with the rest. leaders of the rebellion. First, they tried to dismember him, where his limbs were tied to four horses, but when they failed, they sent him to behead the indigenous uprisings were controlled by the Spanish monarchy, but these influenced future independence fights.