The history of the area, named after the Quijos people, dates back to a commission sent there by the Sapa Inca Túpac Yupanqui to investigate the existence of gold deposits.

By the time the city of Quito was founded in 1534, the existence of the Quijos was already known to the Conquistadores, with the first Spaniards arriving in 1538 in the search for El Dorado and La Canela.

The territory was formally established as part of the Spanish Empire by Andrés Hurtado de Mendoza, 3rd Marquis of Cañete, then Viceroy of Peru, on September 9, 1559, from his seat in Lima.

[1][3] With the creation of the Republic of Colombia in 1819, during the Spanish American Wars of Independence, the new state claimed the area of the governorate.

[1] Meanwhile, Peru had incorporated the General Command of Maynas (of which Quijos was part of, excluding the village of Papallacta, due to the real cédula of 1802)[4] into its Department of Trujillo by 1825.