Microbial contamination and damaging effects due to environmental factors (temperature, humidity) of old books is an extremely important issue in the heritage preserving field, being a great threat to this unique cultural and literary treasure. This paper analysed the indoor environmental conditions, the microbiological characteristics of the air and the condition itself of 27 clerical books (from eighteenth to nineteenth centuries), randomly chosen from the library of Bistrița Monastery, Romania. The analysis revealed that most of the books were contaminated and damaged by moulds and yeasts. The statistical analysis (chi-square test) shows that the incidence of mould species was not coincidental. The most common isolated fungi discovered on old books were Penicillium spp. (40.7%), Cladosporium spp. (33.3%) and Fusarium spp. (29.6%). Fungal contamination was observed in 17 books. Microbiota air tests have shown possible contamination by air flow. Often, the measured temperature/humidity values are not in line with the requirements of the legislation in force, especially during the cold seasons, the average minimum temperature varying from 3 to 6 °C to an average maximum temperature of 22–25 °C; the values of relative humidity were between 27 and 77%. In terms of storage conditions, the recorded values of temperature and humidity are extremely harmful to the stored documents. Therefore, these indoor environmental conditions have to be improved, in order to reduce/eliminate potential sources of fungal contamination and to achieve optimal environmental preserving conditions.