The aim of this work was to study the diversity and spatiotemporal fluctuations of airborne fungi in the National Library of Greece after its relocation from the Vallianeio historic building in the center of Athens to entirely new premises at the Stavros Niarchos Foundation Cultural Center, and also to compare the fungal aerosol in between the two sites. The air mycobiota were studied by a volumetric culture-based method, during the year 2019 in order to assess their diversity and abundance and to compare with those previously reported in the historic building. Twenty-eight genera of filamentous fungi were recovered indoors and 17 outdoors, in addition to yeasts registered as a group. The number of fungal genera recovered was almost similar in both premises, whereas seventeen genera indoors were identical, dominated by Penicillium, Cladosporium and Aspergillus. The mean daily fungal concentration was found to be 66 CFU m−3 indoors and 927 CFU m−3 outdoors in the new location vs 293 and 428 CFU m−3 indoors and 707 and 648 CFU m−3 outdoors in the previous one. The mean daily concentration indoors was consistently and significantly lower (P < 0.05) in the new building than in the historic one, although it was higher outdoors. The indoor/outdoor ratio for the total fungi was 0.07 in the new vs 0.41 and 0.66 in the previous one and reveals a superior indoor air quality in the new site. Air temperature and occupancy had a statistically significant impact on the concentration of indoor fungi. The remarkably reduced concentration of the mycobiota in the new premises indicated a considerable decline in fungal burden, mainly due to technological excellency of the facility and continuous preventive measures to ensure an enhanced indoor air quality in the National Library of Greece. This case study provides a paradigm about upgrading of indoor air after re-establishment of a facility in another setting.