Passion fruits, renowned globally for their polyphenolic content and associated health benefits, have enjoyed growing attention from consumers and producers alike. While global cultivar development progresses, Australia has pioneered several native cultivars tailored for its distinct planting conditions. Despite their cultivation, comprehensive studies on the phenolic profiles and antioxidant capacities of these Australian-native passion fruits are notably lacking. This study aims to investigate and compare the polyphenolic content present in the by-products, which are peel (L), and consumable portions, which are the pulp and seeds (P), of four indigenous cultivars: ‘Misty Gem’ (MG), ‘Flamengo’ (FG), ‘Sweetheart’ (SW), and ‘Panama’ (SH). Employing LC-ESI-QTOF-MS/MS for profiling, a comprehensive list of polyphenols was curated. Additionally, various antioxidant assays—DPPH, FRAP, ABTS, RPA, FICA, and •OH-RSA—were performed to evaluate their antioxidant potential. A total of 61 polyphenols were identified, categorized into phenolic acid (19), flavonoids (33), and other phenolic substances (9). In the antioxidant assays, the SHP sample exhibited the highest •OH−-RSA activity at 98.64 ± 1.45 mg AAE/g, while the FGL sample demonstrated prominent DPPH, FRAP, and ABTS activities with values of 32.47 ± 1.92 mg TE/g, 62.50 ± 3.70 mg TE/g, and 57.84 ± 1.22 mg AAE/g, respectively. Additionally, TPC and several antioxidant assays had a significant positive correlation, including DPPH, FRAP, and ABTS. The Australian-native passion fruits revealed distinct polyphenolic profiles and diverse antioxidant capacities, establishing a foundation for deeper health benefit analyses. This study accentuates the significance of understanding region-specific cultivars and their potential nutraceutical applications.