The Botai settlement was discovered in 1980 by archaeologist V. F. Zaibert, a member of the North Kazakhstan Archaeological Expedition. Excavations were carried out with the participation of students from the Petropavlovsk Pedagogical Institute, led at that time by Rector Shakenov Kanash Shakenovich.

The first excavations at the settlement yielded up to 40,000 artifacts for domestic science. Subsequently, the settlements of Krasny Yar, Vasilkovka IV, Roshchinskoye, Balandino, and Sergeyevka were discovered. In the 1980s, while studying these Eneolithic settlements, V. F. Zaibert concluded that a new archaeological culture should be identified — the Botai culture. Both the settlement and the archaeological culture were named after one of the leaders of local Kazakh clans. In the early years of research, the North Kazakhstan Archaeological Expedition excavated 7,528 square meters of the cultural layer.

In the summer of 1983, an All-Union field archaeological seminar was held at the Botai excavation site. Between 1984 and1985, the team of archaeologists from the North Kazakhstan Archaeological Expedition achieved significant results. In 1985, a joint article by V. F. Zaibert and O. I. Martynyuk titled “Ceramic Complexes of the Eneolithic Botai Settlement” was published, which proposed that Botai ceramics originated from the Neolithic pottery of the Atbasar culture.

In 1985, the materials by I.L. Chernai «Textile craft and ceramics based on materials from Eneolithic-Bronze Age monuments of Southern Trans-Urals and Northern Kazakhstan», V.I. Zaitov «Characteristics of stone tools from the Botai settlement», T.A. Danilenko «Bone inventory of the Botai settlement», V.F. Zeibert, A.A. Pleshakov «Cutting tools of the Botai settlement» were published.. A general characterization of the Botai culture was presented in V. F. Zaibert’s publication “The Botai Settlement and the Tasks of Studying the Eneolithic of Northern Kazakhstan.”

In 1994, Professor V. F. Zaibert delivered a series of lectures on Botai at several universities in the United Kingdom. In the same year, an exhibition dedicated to the Botai culture was also held at the Cambridge Archaeological Museum as part of the international symposium “Early Horse Breeders of Eurasia,” attended by 80 scholars from 16 countries.

In 1996, joint Kazakh–German research on Botai materials began. The materials from the Botai settlements were studied using traditional archaeological methods such as traceology, typology, osteometry, radiocarbon dating, and geomagnetic surveying. In the early 1990s, geomagnetic research was carried out with the support of international specialists. At the same time, laboratories in Cambridge, Oxford, Bristol, and Exeter conducted analyses of organic residues preserved on pottery. These studies revealed traces of dairy fats, providing important insights into the diet of Botai people.

Significant contributions to the study of horse domestication at Botai were made by L. N. Makarova, T. N. Nurumov, and S. S. Kaliyeva, as well as international researchers including L. L. Gaiduchenko (Chelyabinsk, Russian Federation), S. Olsen (Carnegie Museum of Natural History, USA), D. Anthony and D. Brown (Hartwick College, USA), N. Benecke and A. von den Driesch (Germany), M. Levine (Cambridge, United Kingdom), A. Outram (Exeter, United Kingdom), R. Bendry (Winchester, United Kingdom), A. Kasparov (Russian Academy of Sciences), and D. Orlando.

From the mid-1990s onward, research activity slowed, but archaeological excavations at the site continued on a regular basis.

In 2000, the Botai settlement became part of the State National Natural Park “Kokshetau.” In 2001, a protected zone with a total perimeter of 3,600 meters was established around the site. Fencing was installed to prevent damage from livestock and vehicles. Between 2005 and 2006, part of the artifacts discovered at Botai were transferred to the Central State Museum of the Republic of Kazakhstan in Almaty.

Researchers from Kokshe Academy made an important contribution to the study of the Botai culture within the framework of the national program on the study and preservation of Kazakhstan’s historical and cultural heritage (2004–2006). The results of the Kokshetau Archaeological Expedition were presented in the collective monograph “Secrets of the Ancient Steppe.”

In 2009, an article was published in the international journal Science, stating that the earliest evidence of horse domestication was found at the Eneolithic Botai settlement and that the Botai people produced kumis. Between 2007 and 2011, archaeological excavations were suspended, and this period was used for conceptual analysis of the Botai culture. In 2011, V. F. Zaibert published the comprehensive monograph “Botai: The Origins of Steppe Civilization.”

In 2017, Alan Outram applied a new mass spectrometry method to identify proteins preserved in dental remains. In the same year, E. Ananyevskaya (Vilnius, Lithuania) conducted tests on samples for miliacin.

In 2017, the Botai archaeological site was included in the State List of Sacred Sites of Kazakhstan. It was also incorporated as a key research object within the new national program “Rukhani Zhangyru.” A project titled “Reconstruction of Socio-Economic and Worldview Aspects of the Botai Culture, Including Sacred Contexts” was developed. In 2018, with the support of the Kazakh Research Institute of Culture of the Ministry of Culture and Sports of the Republic of Kazakhstan, the monograph “Sacred Contexts of the Botai Culture” by Professor V. F. Zaibert was published. On November 21, 2018, in the article by the former President of the Republic of Kazakhstan, Nursultan Nazarbayev, titled “Seven Facets of the Great Steppe,” Botai was highlighted as an important context in the formation of equestrian culture.

The result of many years of research was the establishment in 2018 of the State Historical and Cultural Museum-Reserve “Botai,” which preserves and presents this unique heritage to the public.