Monitoring the indoor microclimate in old buildings of cultural heritage and significance is a practice of great importance because of the importance of their identity for local communities and national consciousness. Most aged heritage buildings, especially those made of wood, develop an indoor microclimate conducive to the development of microorganisms. This study aims to analyze one wooden church dating back to the 1710s in Romania from the microclimatic perspective, i.e., temperature and relative humidity and the fungal load of the air and surfaces. One further aim was to determine if the internal microclimate of the monument is favorable for the health of parishioners and visitors, as well as for the integrity of the church itself. The research methodology involved monitoring of the microclimate for a period of nine weeks (November 2020–January 2021) and evaluating the fungal load in indoor air as well as on the surfaces. The results show a very high contamination of air and surfaces (>2000 CFU/m3). In terms of fungal contamination, Aspergillus spp. (two different species), Alternaria spp., Cladosporium spp., Mucor spp., Penicillium spp. (two different species) and Trichopyton spp. were the genera of fungi identified in the indoor wooden church air and Aspergillus spp., Cladosporium spp., Penicillium spp. (two different species) and Botrytis spp. on the surfaces (church walls and iconostasis). The results obtained reveal that the internal microclimate not only imposes a potential risk factor for the parishioners and visitors, but also for the preservation of the wooden church as a historical monument, which is facing a crisis of biodeterioration of its artwork.