This protocol investigates the relationship between indoor air quality (IAQ) and respiratory health as well as academic performance in students. The effects of air purifiers in real-world educational settings on lung health and academic outcomes have not been extensively studied. Our objectives are to: (1) evaluate the effectiveness of low-cost air purifiers in improving IAQ; (2) assess their impact on children's lung function; and (3) examine their influence on academic performance. This prospective, pragmatic controlled trial involves students from two schools in central-southern Chile, with three classrooms at each school equipped with air purifiers over three weeks. IAQ is initially measured without purifiers, followed by two weeks of alternating between purifier models "A" and "B," with participants blinded to the brand of the devices. Measured outcomes include IAQ (PM 2.5, PM 10), lung function (peak flow measurements), and cognitive performance (memory, attention, language, and problem-solving). Confounding factors are controlled through guardian questionnaires and evaluations of outdoor air quality and weather conditions. Ethical approvals are obtained, and data collection is conducted during the winter of 2023.•A pragmatic controlled trial involving middle school students monitored and intervened during three weeks in selected classrooms to evaluate the impact of air purifiers.•Classrooms were equipped with air purifiers, and indoor air quality and thermal comfort was assessed both with and without the intervention, employing randomization and a blinding method for purifier brands in use.•Key outcomes on students were measured weekly, including environmental conditions, lung function, and academic performance.