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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 800 ppm [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].