Grafting in tomatoes is widely used to increase tolerance to biotic and abiotic stresses and productivity. Divergent information is available on the impact of somatogenetic interactions between rootstock and scion on the nutritional status and fruit quality attributes of tomato. The productivity of tomato grafting and produce quality are also influenced by agronomic practices such as production systems and growing environments. This study evaluated the effects of grafting on metabolic traits contributing to the quality of fruits grown in protected (high tunnel, HT) and unprotected (open field, OF) production systems across three Texas environments (Overton, Uvalde, and Weslaco) during two spring seasons. Grafted combinations included two rootstocks ("Estamino" and "Multifort") and two scions ("TAM. Hot Ty", "Tycoon" in 2017; and "TAM Hot Ty", "HM1823" in 2018). Over the two seasons, fruits of grafted tomato plants exhibited a 10−18% reduction in ascorbic acid (vitamin C) content, but total soluble solids (TSS), titratable acidity (TA), and most metabolites such as sucrose, glucose, fructose, polyphenol, and carotenoids (lycopene, β-carotene, lutein) were unaffected by grafting. Conversely, the production system (HT vs OF) significantly influenced fruit quality traits with HT increasing lycopene (36%), β-carotene (20%), fructose (16.7%), glucose (14.3%), and TSS/TA (B/A ratio) (22%) as compared to OF in the 2017 season but not 2018. Tomato fruit quality was also impacted by the environment and its interactions with production systems. In the 2017 growing season, Uvalde grown fruits possessed significantly higher carotenoids and lower vitamin C, whereas in 2018 lycopene, β-carotene, and vitamin C content were lowest in Uvalde fruits compared to other environments. A significant environmental variation in the accumulation of carotenoids (lycopene, β-carotene, and lutein) and ascorbic acid was observed among growing environments. The study suggests that metabolic traits related to fruit quality in tomato are mostly affected by the production system and growing environments.