Global climate changes involve elevated atmospheric [CO2], fostering the carbon allocation to tree sink tissues, partitioning it into metabolic pathways. We use metabolomics analysis in adult and juvenile needles of four Pinus pinaster genotypes exposed to two levels of growth [CO2]: ambient (400 μmol mol-1) and enriched (800 μmol mol-1), to know if the metabolic responses are genotype-dependent and vary according to the stage of needle ontogeny. The eCO2-induced changes in the needle metabolomes are more significant in secondary metabolism pathways and especially meaningful in juvenile needles. The heteroblasty has important consequences in the expression of the metabolome, and on the plasticity to CO2, determining the level of specific metabolite accumulation, showing an interdependence between adult and juvenile needles. The P. pinaster needle metabolomes also show clear quantitative differences linked to genotype, as well as regarding the metabolic response to eCO2, showing both, common and genotype-specific biochemical responses. Thus, the changes in flavonol levels are mainly genotype-independent, while those in terpenoid and free fatty acids are mainly genotype-dependent, ratifying the importance of genotype to determine the metabolic response to eCO2. To understand the adaptation mechanisms that tree species can develop to cope with eCO2 it is necessary to know the genetically distinct responses within a species to recognize the CO2-induced changes from the divergent approaches, what can facilitate knowing also the possible interrelation of the physiological and metabolic responses. That could explain the controversial effects of eCO2 on the carbon-based metabolite in conifers, at the inter- and intra-specific level.