In this work, the impact of terroir, cultivar, seasonality, and farming systems on functional traits of tomato was hierarchically investigated. Untargeted metabolomics, antioxidant capacity, colorimetric assays, and enzyme inhibition were determined. The total phenolic and carotenoid contents significantly varied between growing years, whereas an interaction between the farming system and growing year (p < 0.01) was observed for total phenolics, carotenoids, and flavonoids, and for acetylcholinesterase inhibition. Hierarchical clustering showed that geographical origin and growing year were the major contributors to the differences in phytochemical profiles. Nonetheless, supervised modeling allowed highlighting the effect of the farming system. Several antioxidants (L-ascorbic acid, alpha-tocopherol, and 7,3 ',4 '-trihydroxyflavone) decreased, whereas the alkaloid emetine and phytoalexin phenolics increased under organic farming. Taken together, our findings indicate that cultivar and pedo-climatic conditions are the main determinants for the functional quality of tomato, whereas the farming system plays a detectable but hierarchically lower.