Several factors explain the Spaniard conquest of the Inca. First, and most important, was the fact that the Spaniards carried diseases that ravaged the Inca population in advance of the arrival of the Spaniards. This obviously led to upheaval, and was exacerbated because among the dead was the Inca emperor and his successor. A civil war ensued for control of the throne, with Atahuallpa emerging victorious. But the Spaniards encountered a population devastated by disease and both divided and exhausted by war. The Spaniards also had other advantages, including armor that was effective against Indian clubs and other weapons. They carried crossbows, steel blades, arquebuses and other weapons that sliced through the Inca's quilted armor. They also had horses, which gave them a major advantage. Additionally, the fact that the Inca had no writing system meant that they had no real knowledge of the geopolitics that had brought the Spaniards to South America. Atahuallpa could assume that his effort to bribe Pizarro to leave would be successful. He had no way of knowing that Pizarro was part of a larger imperial project.
Source: Diamond, Guns, Germs, and Steel, 74-80.