Problems in the degradation and biodegradation of cultural heritage objects exposed or stored in public buildings and museums and of construction materials are caused (between others) by the activity of microorganisms. Biodeterioration can be observed not only at the level of the building materials of museum buildings, but also at the level of materials from which art objects are made (natural or artificial) and is determined by factors such as the chemical composition and nature of the composition material, the microclimate characteristics and exposure objects, but also through the manner and frequency of surface cleaning and housekeeping in museums. Based on this, the present study offers, through classical methods, a qualitative and quantitative identification of microorganisms inside a heritage museum building located in a temperate climate country. The purpose of the work was to determine to what extent the bacteriological microflora inside can directly and indirectly contribute to the health quality of the building’s occupants as well as the degradation of its materials and structures. The results emphasize the presence of some fungi and bacteria, among them Alternaria spp., Aspergillus spp., Penicillium spp., Cladosporium spp., and Botrytis spp. All of the analyzed rooms have a high and very high degree of fungal contamination (between 524 and 3674 UFC/m3), which can represent a danger to both human health and the integrity of the exhibitions. This is more pronounced considering that some of species of fungi identified are associated with sick building syndrome, problems in humans due to harmful exposure to viruses, bacteria, and pathogens, which generate possible symptoms such as rhinorrhea, nasal congestion, hoarseness, coughing, sneezing, and irritability for the personnel and visitors.