We study the dynamics of a naturally ventilated room in which a point source provides a steady source of buoyancy and which is affected by an opposing unsteady wind. The wind is modelled as a stochastic forcing, which aims at simulating realistic velocity fluctuations as observed in the lower atmosphere. Our main finding is the occurrence of a “noise-induced transition”, namely a structural change of the mean behaviour of the system: the warm–cold air interface does not fluctuate around the elevation exhibited when wind is constant, but oscillations occur around a new (significantly lower) interface elevation. We provide the physical explanation for such a counter-intuitive behaviour and show its dependence on (i) wind characteristics (intensity and timescale of fluctuations) and (ii) relative strength of wind over thermal loads. A realistic example case shows that the behaviour highlighted here has potentially major implications in the design and management of naturally ventilated buildings. •Topic: natural ventilation of rooms (point buoyancy source) forced by stochastic wind.•We compare the system response to stochastic and constant winds (same mean velocity).•Mean configurations attained under constant and fluctuating wind are very different.•Wind fluctuations induce a worsening of the ventilation performance of the room.