The indoor climate quality in classrooms at the University of Coimbra, Portugal, was investigated as part of the 3SqAir project, supported by the Interreg SUDOE program. This research focused on two equipped classrooms with different ventilation systems: natural and mechanical ventilation. Both classrooms were continuously monitored for IEQ parameters: thermal comfort, indoor air quality, noise, and lighting during heating and cooling seasons. Air temperature, relative humidity, CO₂ concentration, particulate matter, nitrogen dioxide, volatile organic compounds, formaldehyde, sound pressure level, and illuminance were measured. Outdoor weather conditions were also recorded. The primary focus was on air temperature, CO₂ concentrations, and relative humidity, while air change rates (ACH) were estimated using the Tracer Gas Method. The results showed inadequate thermal conditions in both classrooms, particularly during the heating season. Most weekly mean CO₂ concentrations were within acceptable limits, while ACH were below standard recommendations in four CO₂ decay phases. Simulations of CO₂ decay revealed further air quality gaps in each room. Corrective measures within the 3SqAir project framework were suggested for approval and implementation while monitoring continues. This work represents the first phase in an evolving study towards developing sustainable strategies for improving indoor air quality in classrooms.