Ground-level ozone is a priority air pollutant, causing ~ 22,000 excess deaths per year in Europe1, significant reductions in crop yields2 and loss of biodiversity3. It is produced in the troposphere through photochemical reactions involving oxides of nitrogen (NOx) and volatile organic compounds (VOCs). The biosphere is the main source of VOCs, with an estimated 1,150 TgC yr−1 (~ 90% of total VOC emissions) released from vegetation globally4. Isoprene (2-methyl-1,3-butadiene) is the most significant biogenic VOC in terms of mass (around 500 TgC yr−1) and chemical reactivity4 and plays an important role in the mediation of ground-level ozone concentrations5. Concerns about climate change and energy security are driving an aggressive expansion of bioenergy crop production and many of these plant species emit more isoprene than the traditional crops they are replacing. Here we quantify the increases in isoprene emission rates caused by cultivation of 72 Mha of biofuel crops in Europe. We then estimate the resultant changes in ground-level ozone concentrations and the impacts on human mortality and crop yields that these could cause. Our study highlights the need to consider more than simple carbon budgets when considering the cultivation of biofuel feedstock crops for greenhouse-gas mitigation.