Organic tomato production is increasing worldwide, thus making necessary the development of varieties adapted to this farming system. It is now well known that the implementation of local tomato plant breeding programs for organic farming is required to increase the performance of varieties in this typology of cultivation regime. In this research, the agronomic performance, nutraceutical contents, and radical scavenging activity of a tomato germplasm line (OSTGL), selected under organically grown conditions, were evaluated for two consecutive years (2018 and 2019) in comparison with the variety ‘Rio Grande’, frequently grown organically in Tunisia. Carotenoids, phenolics, vitamin C, and radical scavenging capacity were assayed spectrophotometrically, while tocopherols were analyzed by HPLC. All data were not affected by year-to-year variability. The OSTGL line showed significantly higher marketable yield, total phenol, flavonoid, vitamin C, α-tocopherol and γ-tocopherol contents, along with radical scavenging activity. The OSTGL red-ripe berries also showed comparable values for average weight, soluble solids, pH, titratable acidity, firmness and coloration, as well as lycopene and β-carotene contents. This open pollinated tomato germplasm line demonstrated to be an effective sustainable variety for improving fruit yield, agronomic, and nutraceutical characteristics under an organic management system.