This study presents numerical simulations analysing the effect of urban heat island (UHI) mitigation measures on the chemical composition of the urban atmosphere. The mesoscale chemical transport model WRF-Chem is used to investigate the impact of urban greening and highly reflective surfaces on the concentrations of primary (CO, NO) as well as secondary pollutants (O-3) inside the urban canopy. In order to account for the sub-grid scale heterogeneity of urban areas, a multi-layer urban canopy model is coupled to WRF-Chem. Using this canopy model at its full extend requires the introduction of several urban land use classes in WRF-Chem. The urban area of Stuttgart serves as a test bed for the modelling of a case scenario of the 2003 European Heat Wave. The selected mitigation measures are able to reduce the urban temperature by about 1 K and the mean ozone concentration by 5-8%. Model results however document also negative secondary effects on urban air quality, which are closely related to a decrease of vertical mixing in the urban boundary layer. An increase of primary pollutants NO and CO by 5-25% can be observed. In addition, highly reflective surfaces can increase peak ozone concentration by up to 12% due to a high intensity of reflected shortwave radiation accelerating photochemical reactions. (C) 2015 The Authors. Published by Elsevier Ltd.