As supreme commander he organized, together with another prestigious general Chalcuchimac, war against Cuzco. Quizquiz was responsible for the significant defeat and capture of Huáscar, where Huáscar planned to use a decoy advance guard that was to be later joined by the body of the army, however this decoy was destroyed before the rest of the army could join it. Defeating in several battles the armies of Huáscar, they achieved the final victory with the storming of the Inca Empire capital. As he was proceeding to the consolidation of power for Atahualpa in the region of Cuzco, the news came of the tragedy of Cajamarca and the capture of his master.