The World Health Organization (WHO) has repeatedly published the health impact of inhabiting spaces with poor environmental conditions. The role of educational institutions is crucial, as they not only contribute to the health of future generations but also raise awareness. Indoor air quality can be one-third to one-fourth worse than commercial or residential buildings. This study highlights the impact of natural ventilation in classrooms on indoor air quality (IAQ). It analyses environmental components primarily sourced indoors, such as CO2 (e.g. occupancy), and others mainly from outdoors, like NO2, PM2.5, and PM10 (e.g. vehicles). A methodology has been developed to evaluate the impact of natural ventilation on air quality, correlating these component values with temperature, relative humidity (RH), and energy consumption. This methodology has been validated through its application in a pilot school chosen for its architectural uniqueness in vertical development and contrasting solar and urban orientations. Despite key findings, such as the relationship between NO2 and PM values and proximity to areas with heavy traffic, natural ventilation remains a viable design strategy. The proposed methodology can guide decision-making in new architectural projects regarding ventilation models.