The relevance of agronomic practices on the nutritional quality greenhouse-grown tomatoes has been recognized. We investigated the influence of (1) cultivar: two local (Pera-Girona and Montserrat) and one commercial (Caramba) varieties; (2) nitrogen dose in nutrient solution (low vs. standard N dose); (3) treatment for plant disease control (sulfur vs. Milsana®) and (4) ripeness (orange vs. full-red color) on levels of carotenoids, phenolic compounds, ascorbic acid and minerals of fruits. Carotenoids and ascorbate were mainly influenced by variety and ripening stage, while N dose slightly affected minerals in fruits; treatments against plant diseases exerted only negligible effects on measured compounds. Local tomato varieties appear more promising as food source of carotenoids, mainly lycopene, and of hydroxycinnamates, such as 5-caffeoylquinic acid and caffeoylquinic derivatives, than commercial variety (total carotenoids: 67.43 mg kg−1 fw vs. 56.34 mg kg−1 fw of Pera-Girona vs. Caramba and total hydroxycinnamates: 90.87 mg kg−1 fw vs. 37.90 mg kg−1 fw of Montserrat vs. Caramba, at full-red color). Tomato variety and harvest maturity of fruit were the main factors affecting nutritional value of tomatoes, while Milsana® treatment did not result in evident nutritional benefits. However, the use of this elicitor might be appropriate considering the increasing environmentally friendly attitudes of consumers.