The recent discovery of large ionospheric disturbances associated with sudden stratospheric warmings (SSW) has challenged the current understanding of mechanisms coupling the stratosphere and ionosphere. Non-linear interaction of planetary waves and tides has been invoked as a primary mechanism for such coupling. Here we show that planetary waves may play a more complex role than previously thought. Planetary wave forcing induces a global circulation that leads to the build-up of ozone density in the tropics at 30–50 km altitude, the primary region responsible for the generation of the migrating semidiurnal tide. The increase in the ozone density reaches 25% and lasts for ∼35 days following the SSW, long after the collapse of the planetary waves. Ozone enhancements are not only associated with SSW but are also observed after other amplifications in planetary waves. In addition, the longitudinal distribution of the ozone becomes strongly asymmetric, potentially leading to the generation of non-migrating semidiurnal tides. We report a persistent increase in the variability of ionospheric total electron content that coincides with the increase in stratospheric ozone and we suggest that the ozone fluctuations affect the ionosphere through the modified tidal forcing.