Interest in organic growing systems that means no harm to the environment, mankind, and the world's natural ecosystem is increasing. This study evaluated the impact of organic versus conventional cultivation method on eggplants (Topan-374 and Pala-49), tomatoes (Rio Grande and Pink), and bell pepper (Kandil dolma) considering individual phenols, total phenol-flavonoid content, antioxidant capacity, and antibacterial potential. Peel and pulp of eggplants were evaluated separately. Organic cultivation enhanced trans-ferulic acid in the peels of both eggplant cultivars and the pulp of Pala-49. Organic Pala-49 had also higher amounts of cyanidin and caffeic acid in the peel, and only caffeic acid in the pulp. Chlorogenic acid was found in higher quantities in organic Rio Grande tomato and bell pepper. All organically grown vegetables in our study had significantly higher total phenol and flavonoid contents than conventional ones except Pink tomato. Organic farming significantly enhanced the antioxidant capacity of both eggplant cultivars. Only organic peel of Pala-49 eggplant cultivar had antibacterial activity against Staphylococcus epidermidis. Organic cultivation has an advantage in terms of antioxidant potential and phenolic constituents, and it enhanced the nutraceutical potential of both cultivars of eggplant, Rio Grande tomato, and bell pepper.