Iridoid blue-based pigments can be found in fruits of genipap (Genipa americana L.). Besides being a potential source of natural blue colorant in the food industry, they have also been associated with pharmacological effects. Therefore, the recovery of iridoids by ultrasound-assisted extraction from both unripe and ripe fruits was analysed by UPLC-DAD-ESI-(-)-QTOF-MS/MS. Nine iridoids were identified from their exact masses and fragmentation pattern, namely geniposidic acid, gardenoside, genipin-1-β-gentiobioside, geniposide, 6′'-O-p-coumaroyl-1-β-gentiobioside geniposidic acid, 6′′-O-p-coumaroylgenipin-gentiobioside, genipin, 6′-O-p-coumaroyl-geniposidic acid and 6′-O-feruloyl-geniposidic acid. Among them, genipin (60.77 mg/g fdw) was found to be the most abundant iridoid in unripe genipap extract, while the ripe genipap extract mainly contained geniposide and geniposidic acid (89.48 and 25.04 mg/g fdw, respectively). It was also observed that the iridoids of the unripe genipap extract are able to scavenger DPPH, ABTS and peroxyl radicals as well as exerting a cytostatic effect against both glioma and breast cancer cell lines. This study provided information about the properties of unripe and ripe genipap extracts which can be used as a reference for further studies focusing on the potential application of G. americana L. in commercial products containing natural blue colorant with functional claims.