Almost all hospitals are equipped with air-conditioning systems to provide a comfortable environment for patients and staff. However, the accumulation of dust and moisture within these systems increases the risk of transmission of microbes and have on occasion been associated with outbreaks of infection. Nevertheless, the impact of air-conditioning on the transmission of microorganisms leading to infection remains largely uncertain. We conducted a scoping review to screen systematically the evidence for such an association in the face of the coronavirus disease 2019 epidemic. PubMed, Embase and Web of Science databases were explored for relevant studies addressing microbial contamination of the air, their transmission and association with infectious diseases. The review process yielded 21 publications, 17 of which were cross-sectional studies, three were cohort studies and one case−control study. Our analysis showed that, compared with naturally ventilated areas, microbial loads were significantly lower in air-conditioned areas, but the incidence of infections increased if not properly managed. The use of high-efficiency particulate air (HEPA) filtration not only decreased transmission of airborne bioaerosols and various microorganisms, but also reduced the risk of infections. By contrast, contaminated air-conditioning systems in hospital rooms were associated with a higher risk of patient infection. Cleaning and maintenance of such systems to recommended standards should be performed regularly and where appropriate, the installation of HEPA filters can effectively mitigate microbial contamination in the public areas of hospitals.