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The nutritional and functional quality of eggplants is heavily influenced by cultivar selection and fertilization techniques. This study evaluated the effects of cultivar, grafting, and fertilization regime on the nutritional and functional quality of eggplant (Solanum melongena L.) cultivated under plastic tunnel conditions. Two commercial hybrids (Mirval and Black Pearl) were assessed under two grafting treatments (Solanum sylvatica and Rezistar F1) and three fertilization regimes: biological (Micoseed®), organic (Orgevit®), and chemical (Nutrispore®), with ungrafted and unfertilized plants used as controls. Fruit samples were analyzed for total polyphenol content (TPC), antioxidant capacity (ABTS and DPPH assays), chlorophyll a and b, lycopene, and tannin concentrations. Mirval exhibited significantly higher levels of TPC, antioxidant activity, photosynthetic pigments, and lycopene than Black Pearl. Ungrafted plants and those grafted onto S. sylvatica showed superior fruit quality, particularly when combined with organic or chemical fertilization. The highest concentrations of polyphenols (3.61 mg·100 g⁻¹ fresh weight), lycopene (3.18 mg·100 g⁻¹ fresh weight), and total chlorophylls were recorded in Mirval fruits from ungrafted or S. sylvatica-grafted plants under organic or chemical fertilization. These findings indicate that optimizing cultivar–rootstock combinations and fertilization management can significantly enhance the functional quality of eggplant fruits, and support the use of organic fertilization as a sustainable strategy in protected vegetable production systems.