The production environment in the pharmaceutical industry should not be a source of microbial contamination of the product. The purpose of this study was to examine the patterns of changes in the microbial contamination level in cleanrooms. The study was conducted at the educational and scientific Cleanroom Facility of the Biotechnology Department of the Obninsk Institute of Nuclear Power Engineering (IATE NRNU MEPhI). It was shown that the level of contamination of surfaces in a production facility increases with the presence of personnel on the premises. The degree of microbial contamination in the air varies slightly depending on the type of activity and the number of personnel on the premises. The compliance of the investigated Cleanroom Facility with class D for cleanrooms was confirmed. It was concluded that it is necessary to monitor the microbial contamination of premises more often as well as to implement the sanitary treatment in order to eliminate the sources of spore-forming microflora.