It has already been proven that a large portion of the energy consumption gap between simulations and reality is due to the occupant behaviour in buildings. The improving airtightness of buildings makes that Indoor Air Quality (IAQ) can no longer rely on air renewal through infiltrations, bringing the need of ventilation systems. Within this frame, an ongoing dissertation focuses on the relationship between occupancy behaviour and ventilation systems in low energy buildings. In this paper, focus is made on a high rise residential multifamily building in south Germany, which has been retrofitted and then measured for two years to obtain post-refurbishment information. The occupant’s behaviour nature was captured in 27 dwellings by measurements of inside temperatures and window openings and applied to the dynamic simulation environment WUFI+. In addition, a presence estimation model was developed in order to represent user behaviour as close as possible to reality. Different behaviours’ scenarios (concerning window opening, temperature set point, presence, activities) were combined with different control strategies for mechanical ventilation systems, with the aim of analysing the impact of these variables on the energy consumption, thermal comfort and IAQ. The results show that there is a significant energy savings potential that can be achieved regarding to the occupant behaviour, and that the most challenging issue is the trade-off between these energy savings and maintaining healthy environments with higher IAQ. The challenges of the next generation of control strategies for ventilation systems will be to provide high flexibility to make the systems compatible with different user behaviours.