The laboratory was established as part of the Institute of Biochemistry and Physiology of Microorganisms of the USSR Academy of Sciences as a structural unit of the future Institute of Agrochemistry and Soil Science, created a year later. Over the years, the name of the institute transformed into the Institute of Soil Science and Photosynthesis, the Institute of Soil Science and Photosynthesis, the Institute of Fundamental Problems of Biology, and finally, the Institute of Physico-Chemical and Biological Problems of Soil Sciences.

The conceptual task set by Prof. O.V. Makeev before the first team of soil scientists (V.M. Alifanov, A.N. Butsenko, E.G. Gershevich, L.A. Gugalinskaya, A.S. Kerzhentsev, V. Kerzhentseva, S.V. Maksimovich, L.A. Fominykh, O.I. Khudyakov) and later joined by D.G. Fedorov-Davydov was to substantiate cryogenesis as a factor in soil formation. To comprehensively address the problem, permafrost specialists (V.G. Chigir, D.A. Gilichinsky, V.E. Ostrooumov) were invited to the laboratory, a series of meetings on soil cryogenesis were held, and fieldwork was organized. A permafrost research station was established in Transbaikalia at the former base of the Soil Institute, research was initiated in Mongolia (as part of the Soviet-Mongolian biological expedition), in the Chita section of the Baikal-Amur Mainline (stationary), and in the south of Western Siberia.

The results of work in Mongolia (A.N. Butsenko, O.I. Khudyakov, S.V. Maksimovich, L.A. Gugalinskaya, V.G. Chigir) were summarized in O.I. Khudyakov's monograph and in four collective monographs with active participation from S.V. Maksimovich, a 1:2500000 soil map, and the National Atlas of Mongolia.

The research theme in Transbaikalia was "Agricultural Use of Soils with Developed Cryogenesis." At the research station (O.I. Khudyakov, E.G. Gershevich, V.G. Chigir, A.N. Butsenko, V.E. Ostrooumov), a technology for cultivating meadow-swamp soils to grow oats and perennial grasses for haymaking and pastures was developed and tested on a production scale. Based on the results, O.I. Khudyakov published a monograph showing that permafrost, as a climatic formation, influences soil formation at a higher taxonomic rank by forming soils of permafrost and cold formation.

In the southern part of Western Siberia, fieldwork was conducted on river channel shifting issues (D.A. Gilichinsky, A.N. Butsenko, O.V. Makeev, V.G. Chigir, O.N. Gubina). Data on the permafrost-temperature regime of soils and annual heat exchange layer across an extensive territory from the Urals to the Yenisei River (southern taiga-steppe) were obtained and included in the Permafrost Map of the USSR 1:2500000 and the volume "Western Siberia" of "Geocryology of the USSR".

O.V. Makeev was one of the first in soil science to raise the issue of paleocryogenesis, which his son - A.O. Makeev, and students - V.M. Alifanov and L.A. Gugalinskaya, successfully developed. With his participation, an experimental base was created by V.E. Ostroumov, and a scientific direction "physico-chemical cryology of freezing and thawing soils was established.

In 1978, under the leadership of D.A. Gilichinsky, fieldwork began in the eastern sector of the Arctic in collaboration with the Department of Cryolithology and Glaciology of Moscow State University (A.A. Arkhangelsky), which continues to this day. The first participants in these studies were S.V. Gubin, L.A. Fominykh, A.N. Butsenko, V.V. Kiselyova, and from 1984 - D.G. Fedorov-Davydov. The 1980s were challenging for the laboratory - following the Institute, it underwent multiple reorganizations, renamings, and attempts at reprofiling. This included closing work on Kolyma in 1986 and redirecting water through the Volga-Chogray canal, which was supposed to be constructed by a directed nuclear explosion. Only after an article in "Pravda" highlighting the impracticality of the water diversion, did the expeditions continue in the North (led by V.A. Sorokovikov) and the gradual reconstruction of the laboratory began (through a temporary labor collective), culminating under a new director (V.I. Kefeli). The founders were D.A. Gilichinsky, O.V. Makeev, S.V. Gubin, S.V. Maksimovich, V.E. Ostroumov, D.G. Fedorov-Davydov, V.A. Sorokovikov, and A.N. Butsenko. From this point on, a new direction actively developed in the laboratory - biology of permafrost (T.A. Vishnivetskaya, E.V. Spirina, A.V. Shatilovich). The subsequent renaming of the Institute to the Institute of Fundamental Problems of Biology RAS and its work proceeded smoothly and productively.

In 1992, the laboratory held the first International Conference on Cryopedology, which became a tradition: with a 4-year interval, it successfully took place in Syktyvkar, Copenhagen, Arkhangelsk, Ulan-Ude. The international collaboration established at this conference laid the foundation for several circumpolar projects, led to the formation (in 1993) of active working groups on frozen soils in the International Union of Soil Scientists and the International Permafrost Association, and organized soil excursions in Kolyma, the Urals, Alaska, and northern Canada.

In 1991, by order of the Department of Biochemistry, Biophysics, and Chemistry of Physiologically Active Compounds of the USSR Academy of Sciences, the International Paleoecological Expedition "Beringia" was created jointly with the Institute of Ecology and Evolution RAS (A.V. Sher). This marked the beginning of extensive participation of foreign specialists in field research. Despite financial difficulties faced by Russian science, "Beringia" was one of the few post-Soviet expeditions that not only survived but continued its work without interruption, gradually expanding beyond Kolyma and providing continuous monitoring of natural processes in permafrost areas under changing climate conditions.

After the establishment of the Institute of Physico-Chemical and Biological Problems of Soil Science in 2000, the scientific potential of the laboratory increased. E.M. Rivkina - an expert in biogeochemistry of cryolithozone, L.T. Shirshova - who initiated studies on organic matter in frozen soils and rocks, and O.I. Khudyakov - focusing on soil climate, joined the laboratory.

Since 2002, the expedition has been led by A.L. Kholodov, and  new students and graduate students joined the team. The area of work covered the tundra and forest-tundra of the coastal lowlands from the mouth of the Lena River, the lower reaches of the Indigirka and Kolyma rivers to the Klyuchevskaya group of volcanoes in Kamchatka.

Over thirty years, about two hundred students, graduate students, and young specialists have passed through the expedition school. Throughout its history, the expedition has maintained close ties with the Northeast Science Station of the Pacific Institute of Geography of the Far East Branch of the Russian Academy of Sciences in Chersky (S.A. Zimov). Over 100 articles have been published in domestic and foreign journals, and doctoral and candidate dissertations have been defended.

In the mid-1990s, with the assistance of American colleagues, laboratory staff conducted research in the Dry Valleys of Antarctica as part of the American Antarctic Expedition, for which D.A. Gilichinsky, D.G. Fedorov-Davydov, V.A. Sorokovikov, and V.E. Ostroumov were awarded the National Science Foundation Medal. In 2007, the laboratory returned to Antarctica as part of the Russian Antarctic Expedition, carrying out projects during the International Polar Year in ice-free oases on the "Age of Antarctic Permafrost" and "Antarctic Permafrost and Soils." From 2007 to 2010, the younger generation actively participated in permafrost, soil, and microbiological research in Russian Antarctic expeditions. Soil research is conducted jointly with the Institute of Geography of the Russian Academy of Sciences and St. Petersburg State University. Jointly with the Spanish Antarctic Expedition on Deception Island, research on permafrost conditions in areas of active volcanism started on Kamchatka.

Since 2012, E.M. Rivkina has taken over the leadership of the laboratory, and metagenomic methods have been introduced into the arsenal.

In 2020, A.A. Abramov became the head of the laboratory, which was transformed into a department. Geopolitical unrest led to a reduction in the number of staff and the loss of some research directions, but the overall research direction remains unchanged.