The potential of supercritical CO₂ (SC-CO₂) for the extraction of bioactive compounds from mango by-products was assessed. Carotenoid extraction was optimized using a design of experiments based on temperature (35, 55 and 70 °C), pressure (10 and 35 MPa) and co-solvent addition (0%, 10% and 20% of ethanol or acetone). Moreover, the co-extraction of phenolic acids, flavonoids and xanthonoids was evaluated in a subset of parameters. Finally, a comparison was made between SC-CO₂ and a two-step organic solvent extraction of the bioactive compounds from the pulp and peel fractions of two Ecuadorian varieties. The optimal extraction temperature was found to be dependent on the bioactive type, with phenolics requiring higher temperature than carotenoids. The optimal overall conditions, focused on maximal carotenoids recovery, were found to be 55 °C, 35 MPa and 20% of ethanol. The main carotenoid was β-carotene, while phenolics differed among the varieties. The bioactive content of the peel was up to 4.1-fold higher than in the pulp fraction. Higher antioxidant activity was found in the extracts obtained with organic solvents. SC-CO₂ is a promising technology for the isolation of valuable compounds from mango by-products.