The area was inhabited for thousands of years by Amerindians. At the time of European encounter, the Napeano and Iquito peoples occupied the area. They had small seasonal settlements and were nomadic hunter-gatherers, living in close association with the rivers. The city name of Iquitos is derived from a group of native people called Iquitos by the Spaniards. They had previously inhabited areas along the rivers Pastaza, Arabela, Tigre, Nanay, and Curaray. Eventually, the native Iquito migrated to the area around the rivers Nanay, Amazonas, Itaya, and the Lake Moronacocha. Between 1638 and 1769, the Iquitos and other native tribes of the Marañon rivers were obliged to settle down in various Missions (known as reducciones or reductions) founded and run by Jesuit missionaries from the Audiencia of Quito. The Jesuits settled in the major cities of the Audiencia of Quito, which was part of the Viceroyalty of New Granada at the time. During this period of nearly 130 years, 161 Jesuit missionaries worked to convert and educate the natives of the Amazon region. Among them were 63 criollos (white ethnic Spanish colonists born in the Audencia), 43 Spaniards, 32 Germans and Dutch, 20 Italians, 2 Portuguese, and 1 Frenchman. Their role in South America was to convert the natives of the Amazon Basin to Christianity. The Jesuits successfully gathered the natives living along the Marañon river into various Jesuit missions, where they were set to work at farming and other pursuits. Commencing in 1730, the Jesuits took 37 years to found the Iquitos missions along the Marañon River, close to the mouth of the Napo and Amazon rivers. These were collectively known as Iquitos Missions, since all these settlements were mainly populated chiefly by the Iquitos natives of the region. The naming and foundation of all the Iquitos Missions were done by Jesuit Father José Bahamonde. He was born in Quito on 1 January 1710, accepted into the Jesuit order, and served as a missionary for decades. After Charles III of Spain suppressed and expelled the Society of Jesus from South America in 1767, Bahamonde was exiled to Italy, where he died in Ravenna, Italy on 11 May 1786.
During the Spanish Colonial era, most of the Jesuit missions were under the jurisdiction of the Royal Audiencia of Quito. Created in 1563, it was a part of the Viceroyalty of Peru, and was transferred briefly to the Viceroyalty of New Granada on 27 May 1717 known as the Cedula Real of 1717 (Royal Decree of 1717). Six and a half years later, on 5 November 1723, Philip V of Spain dissolved the Viceroyalty of New Granada and reincorporated the Audiencia of Quito into the Viceroyalty of Peru. Sixteen years later Philip V of Spain decided to re-create the Viceroyalty of New Granada and to re incorporate the Audiencia of Quito through the Cedula Real (Royal Decree) dated 20 August 1739. Charles III of Spain suppressed the Society of Jesus, believing them too powerful, and expelled them from South America by order dated 20 August 1767. Given the distance from Quito and the lack of roads connecting to that city, a political vacuum was developed in the area. The undefended Jesuit missions were attacked by the Brazilian Bandeirantes. In response the King of Spain on recommendation of Francisco Raquena created the Government and Commandancy General of Maynas in 1802 to halt the invasion into the Spanish Amazon of land-hungry mestizo Portuguese Bandeirantes. In general, this amounted to the religious administration and military command of all tributaries of the Amazon river in the Amazon Basin that belonged to the Royal Audiencia of Quito in the Viceroyalty of New Granada being transferred again to the Viceroyalty of Peru. The Portuguese advance was halted at Tabatinga.
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