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The release of carbon dioxide (CO₂) into the atmosphere has accelerated during the last two decades. Elevated atmospheric CO₂ concentration (eCO₂) is known as an agent that improves plant photosynthesis. However, eCO₂ was also correlated with alterations in the macronutrient and micronutrient compositions of various dietary crops. In order to explore the effect of eCO₂ on the nutritional and health properties of tomatoes, three parental lines of the Magic population, which includes a large part of the genetic diversity present in large fruit varieties, were used as models. The plants were grown in growth chambers under ambient (400 ppm) or eCO₂ (900 ppm) conditions. The macronutrient and micronutrient contents were measured. The anti-oxidant and anti-inflammatory bioactivities were assessed in vitro on activated macrophages. These analyses highlighted that the carbohydrate content was not affected by the eCO₂, whereas the protein, carotenoid, lycopene, and mineral contents decreased. Regarding the anti-oxidant properties, no influence of eCO₂ exposure was observed. Similarly, the anti-inflammatory properties were not affected by the eCO₂. These data are in contrast with previous studies conducted on different plant species or accessions, indicating that the effect of eCO₂ on crops’ nutrition and health properties is based on complex mechanisms in which growth conditions and genetic backgrounds play a central role.