The early history of the Chácobo Indians is unknown. The first account referring to their existence dates to 1845. The information, provided by missionaries and explorers who traveled through the area during the last decades of the nineteenth century, focuses on the aboriginal peoples' location rather than describing their culture. Documents from 1863 found in the Archive of La Paz refer to the first effort to missionize the Chácobo. Later Jesuit references show that the Chácobo rejected any "invitation" to join the missions, preferring their freedom. Unlike other tribes of the Bolivian Oriente, the Chácobo repelled every early attempt at missionization. Because the northern region of the Llanos de Mojos was an economically uninviting area for colonizers, the Chácobo and most of the neighboring tribes maintained their traditional way of life up to the beginning of the twentieth century.
Until this time, sporadic contacts with outsiders were initiated by the Chácobo Indians only to obtain iron tools. During the last decades of the nineteenth century, however, the discovery of the excellent quality of the rubber tree Hevea brasilienis in the Río Beni region led to the establishment of White populations in those areas considered "uncivilized" or "vacant." And with the White settlements began the extinction of the peoples of the Llanos de Mojos. Extermination came through murderous raids and epidemics that devastated people without resistance to Europeans' diseases. Unwilling to work for rubber patrons as cheap manual laborers, Chácobo Indians migrated to the north of their original area, where they found protection in the open savanna. In reaction to the constant advance of the White population, the Chácobo pattern has always been to move inland rather than either to defend their territory or to share it with White or Creole people. Thus in 1955 the Chácobo were living along the Río Benicito, an area rich in fish and game and isolated from White commercial activities; during the following ten years, missionaries of the Summer Institute of Linguistics (a Protestant organization) moved a portion of the Chácobo population of the Benicito to the Río Ivon, and the rest moved from the Benicito toward the Río Yata. In 1965 both concentrations were still living in these same areas.
The Chácobo traditionally maintained friendly relations with the Cayuvava and the Movima; the former used to visit Exaltación, the closest Jesuit mission to the Chácobo area. As of the 1980s, there is a Chácobo who is married to an old Movima woman. This is the first and only intertribal marriage. Chácobo avoided any kind of contact with the Sirono, whom they considered to be extremely aggressive. Although the Chácobo knew about the existence of the Esse Ejja and the Araona, no contact was established. Currently, Chácobo interact with the Pakahuara, whom they ridicule and consider to be inferior.