Despite the risk of transmission of SARS-CoV-2, Spanish educational centers were reopened after six months of lockdown. Ventilation was mostly adopted as a preventive measure to reduce the transmission risk of the virus. However, it could also affect indoor air quality (IAQ). Therefore, here we evaluate the ventilation conditions, COVID-19 risk, and IAQ in secondary school and university classrooms in Toledo (central Spain) from November 2020 to June 2021. Ventilation was examined by monitoring outdoor and indoor CO₂ levels. CO₂, occupancy and hygrothermal parameters, allowed estimating the relative transmission risk of SARS-CoV-2 (Alpha and Omicron BA.1), H_r, under different scenarios, using the web app COVID Risk^airborne. Additionally, the effect of ventilation on IAQ was evaluated by measuring indoor/outdoor (I/O) concentration ratios of O₃, NO₂, and suspended particulate matter (PM). University classrooms, particularly the mechanically ventilated one, presented better ventilation conditions than the secondary school classrooms, as well as better thermal comfort conditions. The estimated H_r for COVID-19 ranged from intermediate (with surgical masks) to high (no masks, teacher infected). IAQ was generally good in all classrooms, particularly at the university ones, with I/O below unity, implying an outdoor origin of gaseous pollutants, while the source of PM was heterogeneous. Consequently, controlled mechanical ventilation systems are essential in educational spaces, as well as wearing well-fitting FFP2–N95 masks indoors is also highly recommended to minimize the transmission risk of COVID-19 and other airborne infectious diseases.