The Inca arrived in Ecuador in the mid-15th century and imposed their culture. In 1460, Inca ruler Tupac Yupanqui, based in Peru, attacked. The Inca met with resistance from indigenous tribes, and it was several years before the Inca, led by Huayna Capac, defeated them. The Inca introduced their language, Quechua. They also introduced new crops, agriculturual methods.They built cities and a network of roads.

The Spanish fought and defeated the Inca, taking control of Ecuadorian territory. In 1532, Francisco Pizarro and his men came to Ecuador, seeking to conquer the territory. Atahualpa was captured by the Spanish and was held for ransom. He was executed in 1533. Fighting between the Inca and Spanish continued. In 1534, The Inca, led by Rumiñahui, destroyed Quito rather than let it fall to the Spanish. The Spanish capture and killed Rumiñahui, and Quito was refounded. The Spanish based themselves in Lima, Peru, and later, Colombia, governing from Cali, Colombia to Paita, Peru. In 1563, the Spanish named their conquered territory the Audencia de Quito and it was governed by Pizarro's brother.