Subject to religious persecution, Puebloans fled the Spanish Nuevo México territory and cohabitated with the Cuartelejo villagers in the 1600s.

Juan de Ulibarri came to the Arkansas River area of Colorado in 1706 to capture and return Pueblo Native Americans who fled Nuevo Mexico in 1680.

[3][4] Of the 26 archaeological sites, most are from Apache of the Dismal River culture of prehistoric, proto-historic and early historic periods[4] from about 1450 until the mid-1700s.

[9] Silvestre Vélez de Escalante of the Domínguez–Escalante expedition wrote in 1778: In the middle of the last century some families of Christian Indians of the nation and pueblo of Taos rebelled, withdrew to buffalo plains and fortified themselves at a place which afterwards on this account was called El Cuartelejo.

[9]In the 1600s, Puebloan Native Americans revolted against Spanish priests and rulers of Nuevo México,[10][11] who had instituted encomienda, which was a form of slavery.

[12] Throughout the 1600s, Puebloans moved north from what is now New Mexico to live in the Great Plains of western Kansas and eastern Colorado with the Cuartelejo Apache, perhaps as early as 1620.

[9] In 1642, Juan de Archuleta led a Spanish expedition to capture and return the Puebloan Native Americans to Nuevo Mexico.

[5][12][b] Another expedition was led by Juan de Ulibarrí in 1706[10] to return another group of refugees back to Nuevo Mexico.

[8] The Comanche, who rode on horseback, sought to control the Arkansas Valley of what is now eastern Colorado during the early eighteen century.

In the meantime, French and allied Pawnee and Witchita people sought to control land to the east of the valley in Kansas.

[17][18] In 1922, two acres of the Steeles' land that included the pueblo ruins was given to the Kansas Society of the Daughters of the American Revolution (DAR) so that it could be appreciated by the public.

[1][5] They uncovered walls of the pueblo and within the rooms they found animal bones, lithics, ceramics, and a large quantity of corn.

Based upon the presence of charcoal and burnt artifacts within the charred adobe, Williston and Martin believed that it was destroyed by fire.

[1] The Smithsonian Institution excavation of 1939, led by Waldo Wedel,[5] which focused south and north of the pueblo (site code 14SC1).

They found a roasting pit below the pueblo, which meant that people of the Dismal River culture lived there before they cohabitated with the Puebloans.

Artifacts included items from the Dismal River culture, Tewa Polychrome pottery from the southwest, and clay pipes.

[1] Starting with the initial excavation, the archaeological sites have degraded,[17] with damage to the pueblo ruins and removal of artifacts by amateur archaeologists.

[1][17] In 1964, the El Cuartelejo Archaeologist District was made a National Historic Landmark, which protects its resources and resulted in a reconstruction of the walls.

[16][19] Some of the Nuevo Mexico refugees lived with Apache in what is now eastern Colorado at the Arkansas and Purgatoire Rivers, near the site of 19th-century Bent's Fort.

[23] In 1726, Padoucas from Kansas led French traders west to El Cuartelejo, closer to their goal of Nuevo Mexico, where they hoped to establish trade with the Spanish.