Ensuring adequate indoor environmental quality (IEQ) in educational settings is essential for safeguarding students’ well-being and optimizing learning. Despite the importance of this issue, limited research has examined the cross-modal effects of acoustics and indoor air quality (IAQ). In this laboratory study, 29 university students were tasked with assessing soundscapes and evaluating IAQ under two CO2 concentrations (800 and 3000 ppm) and four acoustic conditions (quiet, babble noise, mechanical ventilation noise, and birdsongs). Soundscape data were analysed using linear mixed-effects models, while IAQ assessments were analysed with general linear mixed models. All models accounted for the effects of the sounds, CO2 concentrations, and their interactions. The results revealed that soundscape evaluations were influenced solely by the acoustic conditions, with birdsongs being perceived as pleasant, quiet and calm, mechanical ventilation as monotonous, and babble noise as chaotic. In contrast, IAQ evaluations were affected only by the CO2 concentration, with poorer air quality leading to worse perceptions. In conclusion, for the conditions tested in this experiment, each assessment was independently influenced by its respective domain, suggesting an absence of cross-modal effects.