Due to the dynamic development of industry, related to the processing of plant materials and a subsequent significant increase in the number of employees working in this kind of industry, the indoor air quality is of great importance for the human health. The premises of plants processing plant materials are a specific environment, related to exposure to biological agents. The major sources of microbial contamination of premises are employees’ activities and the operation of devices used in the production process, quality of plant materials, technological processes, construction materials, ventilation (air-conditioning) systems, and outdoor air. Biological agents (primarily bacteria and fungi) transported in the air can cause numerous adverse health outcomes in exposed workers.