The oxidative stability of nutritive and bioactive lipids is essential for their functionality. This study evaluated the potential of lipid fractions from pumpkin seeds obtained from eleven high-performing cultivars of Cucurbita maxima Duchesne, C. pepo L., and C. moschata Duchesne cultivated in Poland, aiming to evaluate their stability for nutraceutical applications. This study investigated the intrinsic relationship between chemical composition and oxidative stability to identify cultivars with promising functional potential and commercial value. The fatty acid, sterol, and lipid antioxidant profiles were characterized using gas chromatography (GC), GC–mass spectrometry (GC-MS), and ultra-high-performance liquid chromatography (UPLC), respectively. Antiradical activity was assessed via the DPPH assay, and oxidative stability was evaluated using differential scanning calorimetry (DSC). The oils exhibited high levels of polyunsaturated fatty acids (PUFAs) (59.5–68.6%), with n-6/n-3 fatty acid ratios ranging from 66.5 to 211.6. The lipid extracts contained up to 97.1% Δ7-sterols, while key antioxidants included squalene (616.6–3092.0 mg/kg) and γ-tocopherol (54.1–423.6 mg/kg). Notably, the C. pepo cultivar ‘Moonshine’ was the least abundant in these bioactive compounds. The carotenoid content ranged from 5.7 to 19.4 mg/kg across the extracts. Among the studied cultivars, ‘Show Winner’ and ‘Pink Jumbo Banana’ (C. maxima) stood out as promising candidates for nutraceutical applications due to their elevated levels of tocopherols, carotenoids, and squalene. A moderate n-6/n-3 fatty acid ratio (100–170), coupled with balanced levels of γ-tocopherol and squalene, was found to significantly enhance the oxidative stability of pumpkin seed lipids. These lipid fractions also show potential as stabilizing additives for oils rich in α-linolenic acid but deficient in natural antioxidants.
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