The Faculty of Food Sciences has its roots at the Faculty of Dairy Technology and Cheese-making established in 1945 at the Tertiary School of Rural Management in Cieszyn. In 1950, the Faculty of Dairy Technology was moved to the newly established Tertiary College of Agriculture in Olsztyn. With the development of the Olsztyn College, the Faculty went through consecutive stages of transformations. According to the Decision by the Minister of Tertiary Education the organizational structure of the Faculty in 1950 consisted of the: Chair of Milk Chemistry and Dairy Products, Chair of Technical Microbiology, Chair of Dairy Technology, Chair of Dairy Machines and the Chair of Dairy Industry Economies and Organization. During that year the faculty had 177 students. In 1957, two new organizational units were established: Chair of Mathematical Statistics and Mathematics and Chair of Physics while in 1958 the Chair of Food Technology and Storage Industry was added. During that year the Faculty had 260 students. Until 1957 the Faculty offered 3.5-year 1st degree studies. The 2nd degree studies at the Faculty were initiated during the academic year of 1957/1958.

In 1965, the Faculty obtained the rights to confer the degree of Ph. D. in technology and in 1966 it changed its name to the Faculty of Dairy and Food Technology. In 1970, 3 new organizational units were established: Institute of Food Engineering and Biotechnology, Institute of Food Physics and Chemistry and Chair of Food Industry Economies and Organization. Three years later, in 1973, the Faculty name was changed to the Faculty of Food Technology.

In 1998, the Faculty, as the first one in the country, changed its name to the Faculty of Food Sciences and in 1999 it became a part of the newly established University of Warmia and Mazury in Olsztyn.