The COVID-19 pandemic increased the awareness and importance of infectious pathogens as contaminant in the indoor air, especially for non-residential buildings with a high occupational density like schools. During the COVID-19 pandemic air cleaning is often proposed as mitigation strategy for infectious risk in these type of buildings. However, indoor air quality (IAQ) in general comprises of a large range of possible contaminants and factors that can equally impact the health, comfort and well-being of occupants. In this context, a study was conducted in Flanders (Belgium) with the aim of investigating the potential impact of ventilation and air cleaning on the IAQ and infection risk control in Flemish public spaces. This paper describes part of this larger study, focusing on the assessments carried out in two primary schools. In the first school, which did not have a mechanical ventilation system, 4 classrooms were assessed for three weeks. In the second school, 4 classrooms with centralized mechanical ventilation system were assessed in two separate measurement campaigns of 3 weeks. Between the two measurement campaigns in school 2, the defects in the mechanical ventilation system which were observed during the first campaign were corrected. In each school, in three of the four classrooms, specific interventions were done after the first week of monitoring, among which the introduction of air cleaners. A fourth class was monitored without intervention. In each classroom, CO2 concentrations, and biological air samples were collected 2 days per week for in-lab qPCR analysis of over 20 genetic markers of respiratory pathogens. The results for SARS-CoV-2.