Heirloom tomato varieties are in demand by consumers due to high antioxidant levels. However, these varieties are difficult to produce and are prone to disease. To overcome these problems, heirloom tomatoes may be cultivated in hydroponic systems and grafted onto disease-resistant rootstocks. However, it is unknown if the antioxidant content and capacity are affected by grafting. In this study, heirloom (Black Krim and Green Zebra) and standard (Big Beef) varieties were grafted onto wild type (WT) or productive rootstocks (Arnold and Supernatural). The tomatoes were harvested at maturity, freeze-dried, and ground into a powder. Lycopene was extracted using hexane, and the content was determined spectrophotometrically at 503 nm. The antioxidant capacity of methanol extracts was evaluated by the 2,2′-azino-di[3-ethylbenzthiazoline sulfonsyr]sulphonic acid (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays, whereas the phenolic content was determined using the Folin–Ciocalteu assay. Interestingly, the grafting of Big Beef and Green Zebra onto Supernatural rootstock resulted in an increased antioxidant capacity, as determined by the DPPH assay. Moreover, the phenolic content was changed for Big Beef grafted onto Arnold, and Big Beef and Green Zebra grafted onto Supernatural. Taken together, these results indicate that certain combinations of standard and heirloom tomato varieties and productive rootstocks may influence the antioxidant capacity and phenolic content. These results may be used to guide producers when choosing rootstocks for cultivating hydroponic tomatoes.