While aspects of indoor environmental quality, such as thermal comfort, indoor air quality (IAQ), acoustic, and visual comfort, are usually studied separately, their interactions are crucial yet often overlooked. Understanding how these factors influence each other is essential for a comprehensive perception of the indoor environment. This paper investigates the relationship between indoor air quality (IAQ) and thermal comfort using an extensive field investigation conducted in university classrooms during the heating season, collecting 712 samples of subjective responses correlated with environmental measurements. Key findings reveal significant correlations between subjective responses related to the thermal environment and those related to air quality. Perceived control over the thermal environment shows stronger correlations with IAQ responses than with thermal responses, particularly with perceived ventilation (r = 0.41), COVID-19 risk (r = 0.28), and air quality (r = 0.28). Additionally, environmental parameters demonstrate stronger correlations with thermal responses than with IAQ responses. Higher CO2 concentration is associated with increased thermal sensation and decreased thermal preference and perceived control. Conversely, IAQ responses remain relatively stable with changes in indoor operative temperature. The difference between the operative temperature to which the occupants are exposed and their expressed neutral temperature widens as CO2 concentration rises, indicating a reduced adaptive capacity of occupants which is associated with increasing CO2 levels. These insights are crucial for providing HVAC system management strategies that consider the interaction between different aspects of IEQ, aiming to improve occupants’ well-being and reduce energy consumption.