The grafting of fruits and vegetables influences fruit quality. The aim of the present work was to assess the effect of the rootstock and the scion on the antioxidant activity and the content in vitamin C, total phenols, lycopene and β-carotene of bell pepper. The cultivars Fascinato and Jeanette were used as scion and Terrano was used as rootstock. Four harvests in the production cycle of the vegetable were analyzed in a cultivation system under shading nets. The results indicate statistical differences in the content of these bioactive compounds between the varieties, between grafting and not grafting and between sampling dates (p ≤ 0.05). The vitamin C content, β-carotene, and antioxidant capacity proved significantly higher in Fascinato than in Janette. On average, grafting increased β-carotene and vitamin C concentrations and improved the antioxidant capacity, but had no influence on the total phenol or lycopene contents. It is concluded that grafting to the rootstock Terrano improves the nutritional quality of the fruit produced in both varieties of bell pepper studied.