Blood oranges have high concentrations of bioactive compounds that are beneficial to health. In Europe, the cultivation of blood oranges is increasing due to their excellent nutritional properties. InCitruscrops, rootstocks play an important role in juice and can increase the content of bioactive compounds. The morphological, qualitative and nutritional parameters were analyzed in cultivars ‘Tarocco Ippolito’, ‘Tarocco Lempso’, ‘Tarocco Tapi’ and ‘Tarocco Fondaconuovo’ grafted ontoCitrus macrophyllaandCitrus reshni. ‘Tarocco Lempso’ grafted ontoCitrus macrophyllaobtained the highest values of weight (275.78 g), caliber (81.37 mm and 76.79 mm) and juice content (162.11 g). ‘Tarocco Tapi’ grafted ontoCitrus reshniobtained the most interesting qualitative parameters (15.40 °Brix; 12.0 MI). ‘Tarocco Lempso’ grafted ontoCitrus reshniobtained the most intense red juice (a*= 9.61). Overall, the highest concentrations of primary metabolites were in proline, aspartate, citric acid, and sucrose. The results showed that ‘Tarocco Ippolito’ juice grafted ontoCitrus reshnihad the highest levels of total hydroxycinnamic acids (263.33 mg L−1), total flavones (449.74 mg L−1) and total anthocyanins (650.42 mg L−1). To conclude, ‘Tarocco Lempso’ grafted ontoCitrus macrophyllaobtained the best values of agronomic parameters, and the cultivars grafted ontoCitrus reshniobtained significantly higher concentrations in primary and secondary metabolites.