The impact of elevated carbon dioxide on plants is a growing concern in evolutionary ecology and global change biology. Characterizing patterns of phenotypic integration and multivariate plasticity to elevated carbon dioxide can provide insights into ecological and evolutionary dynamics in future human-altered environments. Here we examined univariate and multivariate responses to carbon enrichment in six functional traits among six European accessions of Arabidopsis thaliana. We detected phenotypic plasticity in both univariate and multivariate phenotypes, but did not find significant variation in plasticity (genotype by environment interactions) within or among accessions. Eigenvector, eigenvalue variance, and common principal components analyses showed that elevated carbon dioxide altered patterns of trait covariance, reduced the strength of phenotypic integration, and decreased population-level differentiation in the multivariate phenotype. Our data suggest that future carbon dioxide conditions may influence evolutionary dynamics in natural populations of A. thaliana.