Introduction: Allergic bronchopulmonary mycosis (ABPM) is an allergic airway disorder caused by fungal colonization within the respiratory tract. Although pharmacological treatment can lead to temporary remission, the recurrence rate remains high. Therefore, controlling fungal contamination in residential environments is considered essential for both the prevention and management of ABPM and/or other fungus-related allergic airway diseases. The aim of this study was to assess the state of fungal contamination in indoor environments through the observation of volatile organic compounds (VOCs). Methods: Two survey visits were conducted during the autumn seasons of 2020 and 2021 at 17 residences of patients diagnosed with fungus-related allergic airway diseases. VOCs in the indoor air of living rooms were collected using a passive flux sampler over a 24-hour period in principle. Following collection, 23 types of VOCs were quantified by gas chromatography–mass spectrometry and converted to air concentrations using theoretical sampling rates. These VOC concentrations were then compared with the fungal contamination inside air conditioners installed in the respective living rooms. Results: Indoor air concentrations of 23 VOCs—considered to originate from building materials, microorganisms, and the human body—were obtained. No consistent trends were observed in the levels or compositions of VOCs among the 17 residences. However, geosmin concentrations in indoor air showed significant correlations with fungal contamination detected on the heat exchanger (r=0.47, p =0.006) and vents (r=0.37, p=0.034) of the air conditioners used in these residences. Conclusion: Geosmin in indoor air may serve as an indicator of fungal contamination within air conditioner units, which are often not visibly contaminated.