Abstract Increasing bioenergy production is a significant component of European efforts to mitigate climate change, but has contested potential for reducing emissions. We use an integrated land system model to explore the effects of large-scale bioenergy production within the European Union on carbon balances. We find that increased bioenergy crop production is likely to cause substantial deforestation and a commensurate loss of associated carbon stocks largely due to displacement of food production from other areas. Deforestation would occur either within the EU if European forests were not protected, or in other parts of the world arising from indirect land use change if European forests were protected. The net carbon benefit of bioenergy production is largely negative, or uncertain, even under the most optimistic levels of fossil fuel replacement, and will not offset initial carbon losses over the coming 50 yr. The growth of intensive agriculture required to satisfy the demand for bioenergy and food will have negative impacts on crucial ecosystem services. Overall, we identify substantial disadvantages to increasing bioenergy production relative to freeing land for natural succession. At best, large-scale bioenergy production is likely to be irrelevant to time-sensitive climate targets.