Indoor air quality (IAQ) in classrooms significantly impacts the comfort, health, and cognitive performance of students and teachers. The COVID-19 pandemic heightened awareness of IAQ, leading to increasing adoption of mechanical ventilation systems in schools. This study investigates IAQ across 24 primary schools (11 equipped with mechanical ventilation) in the French-speaking region of Switzerland. Concentrations of carbon dioxide (CO2), particulate matter (PM), and volatile organic compounds (VOCs) were monitored during four week-long campaigns spanning from autumn 2021 to winter 2023, partially encompassing the COVID-19 pandemic until February 2022 and heating energy shortages in winter 2023. Supplementary measurements of radon and nanoparticles were performed at selected locations. During school hours, the median concentrations of CO2 and PM2.5 were 560 ppm and 4 µg/m3, respectively (interquartile ranges: 450–780 ppm and 2–6 µg/m3, respectively). Total VOCs (TVOCs) concentrations averaged 41 ± 66 ppb (mean ± standard deviation; integrated measurement including nighttime and weekends). In autumn and winter, classrooms with mechanical ventilation had 20–30 % lower CO2 and TVOC levels compared to naturally ventilated ones. Notably, naturally ventilated classrooms had significantly higher TVOC but lower CO2 levels in winter 2022 than in winter 2023, presumably due to more frequent window opening and cleaning practices tied to COVID-19 regulations. Commonly identified VOCs included acetaldehyde, formaldehyde, acetone, and ethanol. The findings underscore the effectiveness of mechanical ventilation in improving IAQ in schools, while highlighting the influence of seasonal and contextual factors on pollutant levels.