Heritage buildings face risks related to the degradation of exhibited or stored artefacts, up to their destruction over time, as well as the health of workers and visitors. The main causes are microclimatic parameters (temperature, humidity, brightness, particles suspension, pollutants, degree of ventilation or air circulation), biological (bacteria, fungi, molds and insects) and anthropogenic ones (improper maintenance of the building and overcrowding of rooms). In accordance with these, the present study considers a quantitative and qualitative analysis of the air quality and the degree of microbiological contamination of the surfaces and the air inside a synagogue in the municipality of Oradea, Romania. The microbiological study highlighted the presence of some potentially harmful genera of fungi (Alternaria sp., Penicillium sp., Aspergillus sp., Botrytis sp. and Cladosporium sp.) in the indoor air and on the surfaces inside the synagogue; suggesting an average degree of fungal contamination, with possible risk to individual health, especially in children and people with allergic status or allergic respiratory diseases. Statistical analysis concerning the occupational exposure to airborne microbes poses health risks to employees and visitors. Multivariate regression analysis results emphasize that higher symptoms scores were independently associated with experiencing a too low indoor air temperature; these symptoms would disappear within one to two hours after leaving the space. Air pollutants have become part of everyday life; therefore, consistent monitoring of indoor environments offers an effective approach to prevent or minimize the adverse health risk to building occupants in spaces such as heritage buildings.