Atmospheric CO2 concentrations are predicted to double by the end of this century. Although the effects of CO2 fertilisation in crop systems have been well studied, little is known about the specific interactions among plants, pests and pathogens under a changing climate. This growth chamber study focuses on the interactions among Barley yellow dwarf virus (BYDV), its aphid vector (Rhopalosiphum padi) and wheat (Triticum aestivum L. cv. Yitpi) under ambient (aCO2; 400µmolmol–1) or elevated (eCO2; 650µmolmol–1) CO2 concentrations. eCO2 increased the tiller number and biomass of uninoculated plants and advanced the yellowing symptoms of infected plants. Total foliar C content (percentage of the total DW) increased with eCO2 and with sham inoculation (exposed to early herbivory), whereas total N content decreased with eCO2. Liquid chromatography–mass spectrometry approaches were used to quantify the products of primary plant metabolism. eCO2 significantly increased sugars (fructose, mannitol and trehalose), irrespective of disease status, whereas virus infection significantly increased the amino acids essential to aphid diet (histidine, lysine, phenylalanine and tryptophan) irrespective of CO2 concentration. Citric acid was reduced by both eCO2 and virus infection. Both the potential positive and negative biochemical impacts on wheat, aphid and BYDV interactions are discussed.