Simulations of future tropospheric composition often include substantial increases in biogenic isoprene emissions arising from the Arrhenius-like leaf emission response and warmer surface temperatures, and from enhanced vegetation productivity in response to temperature and atmospheric CO2 concentration. However, a number of recent laboratory and field data have suggested a direct inhibition of leaf isoprene production by increasing atmospheric CO2 concentration, notwithstanding isoprene being produced from precursor molecules that include some of the primary products of carbon assimilation. The cellular mechanism that underlies the decoupling of leaf photosynthesis and isoprene production still awaits a full explanation but accounting for this observation in a dynamic vegetation model that contains a semi-mechanistic treatment of isoprene emissions has been shown to change future global isoprene emission estimates notably. Here we use these estimates in conjunction with a chemistry-climate model to compare the effects of isoprene simulations without and with a direct CO2-inhibition on late 21st century O3 and OH levels. The impact on surface O3 was significant. Including the CO2-inhibition of isoprene resulted in opposing responses in polluted (O3 decreases of up to 10 ppbv) vs. less polluted (O3 increases of up to 10 ppbv) source regions, due to isoprene nitrate and peroxy acetyl nitrate (PAN) chemistry. OH concentration increased with relatively lower future isoprene emissions, decreasing methane lifetime by ~7 months (6.6%). Our simulations underline the large uncertainties in future chemistry and climate studies due to biogenic emission patterns and emphasize the problems of using globally averaged climate metrics (such as global radiative forcing) to quantify the atmospheric impact of reactive, heterogeneously distributed substances.