Between the ages of 6 and 18, children spend between 30 and 42 h a week at school, mostly indoors, where indoor environmental quality is usually deficient and does not favor learning. The difficulty of delivering indoor air quality (IAQ) in learning facilities is related to high occupancy rates and low interaction levels with windows. In non-industrialized countries, as in the cases presented, most classrooms have no mechanical ventilation, due to energy poverty and lack of normative requirements. This fact heavily impacts the indoor air quality and students' learning outcomes. The aim of the paper is to identify the factors that determine acceptable CO2 concentrations. Therefore, it studies air quality in free-running and naturally ventilated primary schools in Chile, aiming to identify the impact of contextual, occupant, and building design factors, using CO2 concentration as a proxy for IAQ. The monitoring of CO2, temperature, and humidity revealed that indoor air CO2 concentration is above 1400 ppm most of the time, with peaks of 5000 ppm during the day, especially in winter. The statistical analysis indicates that CO2 is dependent on climate, seasonality, and indoor temperature, while it is independent of outside temperature in heated classrooms. The odds of having acceptable concentrations of CO2 are bigger when indoor temperatures are high, and there is a need to ventilate for cooling.