Although shoot N depletion in plants exposed to elevated [CO₂] has already been reported on several occasions, some uncertainty remains about the mechanisms involved. This study illustrates (1) the importance of characterizing root-shoot interactions and (2) the physiological, biochemical and gene expression mechanisms adopted by nitrate-fed Arabidopsis thaliana plants grown under elevated [CO₂]. Elevated [CO₂] increases biomass and photosynthetic rates; nevertheless, the decline in total soluble protein, Rubisco and leaf N concentrations revealed a general decrease in leaf N availability. A transcriptomic approach (conducted at the root and shoot level) revealed that exposure to 800ppm [CO₂] induced the expression of genes involved in the transport of nitrate and mineral elements. Leaf N and mineral status revealed that N assimilation into proteins was constrained under elevated [CO₂]. Moreover, this study also highlights how elevated [CO₂] induced the reorganization of nitrate assimilation between tissues; root nitrogen assimilation was favored over leaf assimilation to offset the decline in nitrogen metabolism in the leaves of plants exposed to elevated [CO₂].