A single-column chemistry and climate model has been used to study the impact of deforestation in the Amazon Basin on atmospheric chemistry. Over deforested areas, daytime ozone deposition generally decreases strongly except when surface wetness decreases through reduced precipitation, whereas nocturnal soil deposition increases. The isoprene and soil nitric oxide emissions decrease although nitrogen oxide release to the atmosphere increases due to reduced canopy deposition. Deforestation also affects vertical transport causing substantial ozone and hydroxyl changes, also depending on soil moisture. The analysis shows that assessment of the impact of land cover and land use changes on atmospheric chemistry requires the development of explicitly coupled chemistry and meteorological models including surface trace gas exchanges, micro-meteorology and the hydrological cycle.