Research studies have shown the potential effects of indoor environmental quality (IEQ) on pupils’ health and academic performance. The COVID-19 pandemic has prompted renewed interest in the assessment of deficient indoor air quality (IAQ) conditions in schools and has become a priority over achieving adequate comfort conditions. Scientific studies confirm aerosols as one of the transmission routes of SARS-CoV-2 so that the possibility of airborne transmission increases in indoor environments with high occupancy, such as classrooms. As a result, international protocols and guidelines have established a requirement for educational buildings to over-ventilate with a fresh outdoor air supply. The main object of this work is to analyse the effects of the COVID-19 pandemic on thermal comfort and indoor air quality, in winter, in two classrooms of southern Spain. Thus, onsite measurements of environmental variables were conducted before and during the pandemic. Both classrooms have mechanical ventilation systems as they are within a recently built primary school (2018). Results shows a decrease of 300 ppm in CO₂ weekly average values during the pandemic, when hybrid ventilation is used, and a decrease of 400 ppm when schools are naturally ventilated during all teaching hours. However, the analysis of standards shows that over 60% of hours are thermal discomfort conditions.