Since decades, indoor aerosol models have been introduced to understand the behaviour of indoor aerosols. However, studies about model validation in multi-zone form are very rare because of the lack of high quality and well-controlled measurements. We utilized state-of-the-art measurement and modelling approaches to validate the Multi-Compartment and Size-resolved Indoor Aerosol Model (MC-SIAM) inside a two-zone apartment with natural ventilation. According to the MC-SIAM simulations, the ventilation rates ranged from 0.06 to 0.31 h–1 during closed windows and it was as high as 2.1 h–1 when a window was open; compared to the tracer gases analysis results, the ventilation rate was as high as 0.26 h–1 (closed windows) and 1.7 h–1 (open window). The internal airflow predicted with the MC-SIAM ranged from 9.3 to 11 m–3 h (tracer gas analysis 7.6–15 m–3 h) when the door between the internal rooms was opened. The methods utilized in this study have proven that indoor aerosol models such as the MC-SIAM are valid to describe the behaviour of indoor aerosol particles inside multi-zone dwellings with the assumption of well-mixed indoor air inside each zone. The next step in indoor aerosol models development should include re-suspension and new particle formation processes.