Allium genus vegetables have significant functional effects on health. In recent years, consumer demand for black forms of these vegetables, produced from fresh Alliums through spontaneous fermentation at high temperature and humidity, has increased, while their functional effects have yet to be fully elucidated. The aim of this study was to compare the antioxidant capacity and total phenol content of various Allium vegetables (yellow onion, red onion, white onion, and garlic) in both their raw and black (fermented) forms. For the production of black onions and black garlic, unpeeled raw forms of these vegetables were kept at 75 °C and 90% humidity for 9 days. Afterward, fresh and fermented samples were lyophilized, dried, and evaluated for total phenol content by the Folin–Ciocalteu method and for antioxidant activity by the ABTS and DPPH methods. The total phenol content increased significantly in all samples after fermentation (p < 0.05), with the highest increases observed in garlic (216%), while the increases in onion species ranged between 44.6% and 118.3%. The increase in antioxidant capacity was also significant in all samples (p < 0.05) and was higher in garlic than in onions. Changes in antioxidant capacity and total phenol content indicate that fermentation improves the nutritional quality of these vegetables.