We lack information on how elevated CO2, and its interaction with other factors like herbivory, affect levels and patterns of trait integration in plants. We experimentally tested the hypothesis that elevated CO2 disrupts and restructures functional associations among plant traits, in the selfing annual, Arabidopsis thaliana. We tested for these effects both in the presence and absence of herbivory by larvae of the diamondback moth, Plutella xylostella. Elevated CO2, both alone and combined with moth herbivory, modified integrated trait responses. In addition, integration under different environments was genotype-specific. These results imply that global changes in CO2 are likely to cause divergent evolutionary outcomes among populations of plants that differ in the initial structure of their quantitative genetic variation.