The Scol'air-FR project is issued from the need to establish an inventory of indoor air quality conditions in primary schools of the canton of Fribourg, Switzerland. In Fribourg, the official trend is to promote mechanical ventilation systems in schools to ensure a good air quality. A properly designed, built, commissioned, and operated mechanical ventilation system should be able to deliver the anticipated flow rate, regardless of who uses it - the only person involved being the person responsible for ventilation system operation. In some cases, however, the expected objectives are not achieved. This similar observation applies to natural ventilation. A good ventilation concept, properly implemented and operated, should also achieve the same objective if the outdoor air quality is good. The aim of this article is to identify differences, in terms of indoor air quality and well-being, between naturally and mechanically ventilated schools. Moreover, we expect to identify if trends are attributable to the operation of ventilation systems or to occupant behaviours. We observed lower carbonic gas levels in building equipped with mechanical ventilation systems. This finding can be extended to VOCs and relative humidity. We also identified different and recurrent issues among the different mechanical ventilation systems. Our results highlight issues measured in buildings equipped by mechanical ventilation systems are mostly related to the balance of the system, while in natural ventilation systems, IAQ related issues are mainly due to the present context and its influences on occupants' behaviour.