Peels and edible pulp from three species of citrus including Citrus aurantifolia (varieties pica and sutil) and Citrus x lemon var. Genova widely cultivated and consumed in Northern Chile (I and II region) were analyzed for phenolic compounds and antioxidant activity for the first time. A high performance electrospray ionization mass spectrometry (HPLC-UV-ESI-MS) method was developed for the rapid identification of phenolics in extracts from peels and juices of all species. Several flavonoids including one kaempferol-O-hexoside (peak 16) and one hesperidin derivative (peak 22) three quercetin derivatives (peaks 4, 19 and 36), five isorhamnetin derivatives (peaks 5, 23, 24, 26 and 29) four luteolin derivatives (peaks 14, 25, 27 and 40), seven apigenin derivatives (peaks 2, 3, 12, 20, 34, 35 and 39), seven diosmetin derivatives (peaks 7-9, 17, 21, 31 and 37), three chrysoeriol derivatives (peaks 10, 18 and 30), and four eryodictiol derivatives (peaks 6, 13, 15 and 38) were identified in negative and positive mode using full scan mass measurements and MSn fragmentations. Ascorbic acid content was higher in the pulps of the varieties Genova and Sutil (60.13 ± 1.28 and 56.53 ± 1.06 mg ascorbic acid per g dry weight, respectively) while total phenolic content was higher in Pica peels followed by Sutil peels (34.59 ± 0.81 and 25.58 ± 1.02 mg/g GAE dry weight, respectively). The antioxidant capacity was also higher for Pica peels (10.34 ± 1.23 µg/mL in the DPPH assay and 120.63 ± 2.45 µM trolox equivalents/g dry weight in the FRAP assay). The antioxidant features together with the high polyphenolic contents can support at least in part, the usage of the peel extracts as nutraceutical supplements, especially to be used as anti-ageing products.