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.

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.

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 the early 19th century, following independence, Peru, Ecuador, Colombia, and Brazil had overlapping claims to the Northwestern Amazon Basin, based on each country's interpretation of their colonial de jure titles.

[16] Walter Ernest Hardenburg, an American engineer that had a prominent role in exposing the Putumayo genocide, also claimed that indigenous people were trafficked in Iquitos and sold in that city for prices ranging between £20 and £40.

[18] In an effort to discourage human trafficking from Loreto to the Brazilian Amazon, government commissioner Joaquin Capello issued a decree in 1900 that required employers to provide a bond for any of their workers that were leaving Peru.

"[21][23] Members of the local business class denied these allegations of trafficking reported by Lores:[21] and in 1904 several rubber merchants signed a petition addressed to the new Prefect Hildebrando Fuentes which demanded the annulment of Capello's decree from 1900.

"[26] The army garrison at Iquitos was sent to the Caraparaná tributary of the Putumayo River in 1908 to assist Arana's company in acquiring several Colombian rubber estates through force.

Two of the most prominent criminals involved in the Putumayo Genocide that were arrested, Armando Normand and Aurelio Rodríguez, escaped from prison at Iquitos in May of 1915 prior to a verdict in their trial.

On 13 August 2012, a special plaque was placed in the plaza 28 de Julio of the city in a ceremony to commemorate the Amazon River and rainforest as one of the Seven Natural Wonders of the World.

[48] In 2021, it was announced that a large (100 MW/100 MWH) solar and storage power facility would be built at Iquitos by 2026, replacing as much as half the diesel burned to produce electricity in the city.

[50] The Itaya and Nanay rivers limit the physical expansion of the city in that direction; new development is growing toward the south and there is a slight population density in Downtown Iquitos.

Geologically, the city is settled in a Tertiary-Quaternary formation lithologically composed by little-consolidated lutites, with remains of flora or fauna, and numerous white-sand lenses of abundant silicon.

The ecosystem is part of the Nanay River basin, specifically in an area called "Ecoregion Napo", which contains unique Amazonian biodiversity, including its distinctive white sand forests.

Some ecologically important animals valued for their rarity in the reserve are the supay pichico (Callimico goeldii), black stump (Callicebus torquatus), equatorial saki (Pithecia aequatorialis) ancient antwren (Herpsilochmus gentryi), Mishana tyrannulet (Zimmerius villarejoi), Allpahuayo antbird (Percnostola arenarum), chestnut-tailed ant (Myrmeciza centuculorum castanea), the pompadour cotinga (Xipholena punicea), saffron-crested tyrant-manakin (Neopelma chrysocephalum), among others.

Two years later, the population increased to about 431 inhabitants and in 1864, there were 648 people, predominantly mestizo due to the presence of families from Borja, Santiago, Santa Teresa, Barranca and others, who fled away from the attack on the Huambisas and Aguaruna native and destroyed the villages.

In 1903, in the middle of the rubber boom, Iquitos had 9,438 inhabitants (census of Benito Lords), of which 542 were foreigners, most of them from Spain (95) Brazil (80), China (74), Portugal (64) and as many from Italy, England, France, Ecuador, United States, Russia, Switzerland and Morocco.

In San Juan Bautista, economic development is based on agriculture (sugar cane, pijuayo, caimito), fish, poultry, livestock (cattle, bubaline) and mining.

With projects of large malls, the city still has a trade-in retail stores and minimarkets throughout the metropolitan area, more strongly in main avenues such as Prospero, Arica, Grau and Alfonso Ugarte located in the center of Iquitos and the Belén District.

While in the international terminal there are flights from/to Panama City on Wednesdays and Saturdays with Copa Airlines also connecting from/to USA, Mexico, Canada, Central America & Caribbean, Colombia, Ecuador, Venezuela and Brazil.

The city also has a wealth of customs and traditions that have remained consistent over the years such as following the Iquitos calendar, celebrating cultural festivities, cuisine, Spanish accent and mythology.

[...] What is striking me is the ease with which iquitenses [sic] engage in conversation with tourists, with a warmth and naturalness that is rarely seen in my native place.Although I'm a veteran of several South American adventures, Iquitos appealed to me as a quirk – a jungle city seems a contradiction and this would be my first Amazon visit to include the cosmopolitan luxuries of a real bed and shops.

With a growing organization of entertainment today, the city has always had groups concerned to project the Iquitos arts such as dance, music, film, painting, literature and theater.

[67][68][69] The most important pioneer of cinema in Iquitos and the Loreto Region is Antonio Wong Rengifo; alongside this, other filmmakers such as Werner Herzog, Armando Robles Godoy, Nora Izcue, Federico García, and Dorian Fernández-Moris prolonged the cinematic presence in the city.

[66] Major films filmed in Iquitos and its surroundings are:[66] Frente del Putumayo (1932) and Bajo el sol de Loreto (1936) by Antonio Wong Rengifo; No Stars in the Jungle (1966) and The Green Wall (1969) by Armando Robles Godoy; Aguirre, the Wrath of God (1972) and Fitzcarraldo (1982) by Werner Herzog; Informe sobre los shipibos (1974), Los hombres del Ucayali and Captain Pantoja and the Special Services (2000) by Francisco Lombardi, and General Cemetery (2012) by Dorián Fernández-Moris.

At first, with Wong Rengifo, was shot slice-of-life/documentary films[66][68][70] Tourism is one of the most vital industries in Iquitos, which has a growing reputation as a honeypot due to its location on the banks of the Amazon River, one of the seven natural wonders of the world.

Iquitos is home to the 120 kilograms (260 lb), bronze commemorative plaque of the Amazon River basin as one of the seven natural wonders of the world, which was granted on 13 August 2012 by Fernand Weber, founder of New7Wonders.

The distinction is shared with Bolivia, Brazil, Ecuador, Suriname, Colombia, Venezuela and French Guiana, however, recognition was given to Peru which originally ran for the Amazon through the Regional Government of Loreto based in Iquitos.

The examples we have of other places are growths of 10, 20 and 30 percent annuallyHowever, despite the great satisfaction, the award caused polarized reactions indicating that the Regional Government of Loreto would be on duty to plan better urban development in Iquitos for the forecasted intense tourism.

[77] The negative scrutiny aimed at disorganized and massive sewer construction was damaging the city streets, causing discomfort and accidents in traffic and littering the aesthetic image of Iquitos.