Fungal growth on cellulose-based materials in libraries can have detrimental effects on books and documents. This biodeterioration affects their physical, chemical, and esthetical characteristics. Thus, this work aimed to assess fungal aerosols’ concentrations and biodeterioration risk in two public libraries with artificial ventilation: the Banco de la República and CAJAMAG libraries. Air sampling was performed using a two-stage viable Andersen cascade impactor with Sabouraud dextrose agar at 4% on Petri dishes. Also, the temperature and relative humidity were measured with a digital thermo-hygrometer HOBO U12 Data Logger. The concentrations were low, with values of around 35 CFU/m3. Aspergillus, Cladosporium, and Penicillium were the predominant genera in the two libraries, with A. niger being the most abundant species. The thermo-hygrometric conditions inside the libraries were stable, with a mean temperature of 25.2 °C and a mean relative humidity of 52.1%. The calculated potential risk associated with fungal aerosols was seen to be medium in both libraries, where Aspergillus genera reported the highest cellulosic activity and hence had a higher risk of biodeterioration.