The objective of this study is to evaluate and compare the quality of oils extracted from yellow and purple passion fruit seeds endemic to Northeast India. In this context, physicochemical properties (acid value, iodine value, etc), thermo physical analysis such as TGA and DSC was performed. Further, the antioxidant properties of seed oils were determined by TPC, TFC, DPPH and ABTS.+ analysis and their interrelation was analysed from Pearson correlation. Lower acid value (2–4.4 mg KOH g−1) and peroxide value (4.2–4.5 mg eq 1000 g−1) confirmed the good quality of oil. The thermal stability of different oils was found to be in the high range of 334.4 °C to 349.5 °C. Fatty acid composition of oils by GC analysis revealed abundance presence of approximately 70% of PUFA and the calculated oxidizability value suggested high oxidative stability in the oils. The universal oil quality score was observed to be high (>50%) when compared to other standard edible oil. Lowest radical inhibitory concentration was observed in yellow passion fruit seed oil from Manipur (70.7 ± 1.7 µg/ml in DPPH and 85.3 ± 5.5 µg/ml in ABTS). Profound antibacterial activity of oils was observed against K. Pneumonia (7.5 ± 0.35 to 12 ± 0.7 cm), B. Subtilis (5 ± 0.7 to 11 ± 0.7 cm), P. aeruginosa (2 to 11.5 ± 0.7 cm) and M. luteus (5 to 10 ± 0.7 cm). This work could add more information on uncommon passion fruit seed oil from Northeast India and further employ in various food and pharmaceutical sectors.