Future climate change is set to have an impact on the physiological performance of global vegetation. Increasing temperature and atmospheric CO 2 concentration will affect plant growth, net primary productivity, photosynthetic capability, and other biochemical functions that are essential for normal metabolic function. Alongside the primary metabolic function effects of plant growth and development, the effect of stress on plant secondary metabolism from both biotic and abiotic sources will be impacted by changes in future climate. Using an untargeted metabolomic fingerprinting approach alongside emissions measurements, we investigate for the first time how elevated atmospheric CO 2 and temperature both independently and interactively impact on plant secondary metabolism through resource allocation, with a resulting “trade-off” between secondary metabolic processes in Salix spp. and in particular, isoprene biosynthesis. Although it has been previously reported that isoprene is suppressed in times of elevated CO 2 , and that isoprene emissions increase as a response to short-term heat shock, no study has investigated the interactive effects at the metabolic level. We have demonstrated that at a metabolic level isoprene is still being produced during periods of both elevated CO 2 and temperature, and that ultimately temperature has the greater effect. With global temperature and atmospheric CO 2 concentrations rising as a result of anthropogenic activity, it is imperative to understand the interactions between atmospheric processes and global vegetation, especially given that global isoprene emissions have the potential to contribute to atmospheric warming mitigation.