It is unclear how sustained increases in temperature and changes in precipitation, as a result of climate-change, will affect crops and their interactions with agricultural weeds, insect pests and predators, due to the difficulties in quantifying changes in such complex relationships. We simulated the combined effects of increasing temperature (by 1.4°C over a growing season) and applying additional rainwater (10% extra per week) using a replicated, randomized block experiment within a wheat crop. We examined how this affected the structure of 24 quantitative replicate plant-aphid-parasitoid networks constructed using DNA-based methods. Simulated climate-warming affected species richness, significantly altered consumer-resource asymmetries and reduced network complexity. Increased temperature induced an aphid outbreak but the parasitism rates of aphids by parasitoid wasps remained unchanged. It also drove changes in the crop, altering in particular the phenology of the wheat as well as its quality (i.e. fewer, lighter seeds). We discuss the importance of considering the wider impacts of climate change on interacting-species across trophic levels in agro-ecosystems.