The research infrastructure IAGOS (In-Service Aircraft for a Global Observing System) equips commercial aircraft with instruments to monitor the composition of the atmosphere during flights around the world. In this article, we use data from two China Airlines aircraft based in Taipei (Taiwan) which provided daily measurements of ozone, carbon monoxide and water vapour throughout the summer of 2016. We present time series, from the surface to the upper troposphere, of ozone, carbon monoxide and relative humidity near Taipei, focusing on periods influenced by the passage of typhoons. We examine landing and take-off profiles in the vicinity of tropical cyclones using ERA-5 reanalyses to elucidate the origin of the anomalies in the vertical distribution of these chemical species. Results indicate a high ozone content in the upper- to middle-troposphere track of the storms. The high ozone mixing ratios are generally correlated with potential vorticity and anti-correlated with relative humidity, suggesting stratospheric origin. These results suggest that tropical cyclones participate in transporting air from the stratosphere to troposphere and that such transport could be a regular feature of typhoons. After the typhoons passed Taiwan, the tropospheric column was filled with substantially lower ozone mixing ratios due to the rapid uplift of marine boundary layer air. At the same time, the relative humidity increased, and carbon monoxide mixing ratios fell. Locally, therefore, the passage of typhoons has a positive effect on air quality at the surface, cleansing the atmosphere and reducing the mixing ratios of pollutants such as CO and <span classCombining double low line"inline-formula">O3</span>.