IENiM was established by the order of the Rector of the University on August 1, 1998 on the basis of the Physics and Mathematics (founded in 1944) and Biology and Chemistry (1961) faculties.

At the time of its formation, the Institute included eight departments (Botany, Zoology and General Biology, Anatomy, Human Physiology and fundamentals of medical knowledge, Chemistry, Mathematics and methods of teaching mathematics, physics and methods of teaching Physics, Philosophy and Sociology, physical culture and sports). Students were trained in pedagogical specialties of higher professional education: Mathematics, Physics, Chemistry, Biology in full-time education, and Biology in correspondence education. Postgraduate professional education was carried out in the following specialties: Solid State Physics and Sociology of Culture, Education and Science.

Currently, training is being carried out in 6 specialties and 3 directions of full-time bachelor's degree and 2 specialties of correspondence education.

The main goal of the Institute, as one of the leading structural divisions of the university, was the development of classical natural science education.