In this study, the effect of fermentation time and baking temperature on the antioxidant activity and phenolic profile of bread enriched with grape and pomegranate seed were investigated. It was determined that total phenolic content (TPC) and antioxidant activity improved through prolonged fermentation time. TPC in the control dough ranged from 280 to 376 mg gallic acid equivalent (GAE)/kg; the TPC in the pomegranate seed-containing dough ranged from 402 to 466 mg GAE/kg; the TPC content in the grape seed-containing dough ranged from 551 to 591 mg GAE/kg. The Trolox equivalent antioxidant capacity (TEAC) value of the control samples increased from 525 to 1,017 mu mol Trolox, the TEAC value of the pomegranate seed-containing samples increased from 1,059 to 2,575 mu mol Trolox, and the TEAC value of the grape seed-containing samples increased from 1,992 to 2,950 mu mol Trolox. The ferulic acid contents in the control, pomegranate seed, and grape seed-containing doughs did not change with increasing fermentation time. However, gallic acid content of the dough increased significantly as the fermentation period increased. It was also determined that baking increased antioxidant activity and gallic acid content showed a 10-fold increase. The TPC and TEAC values in the pomegranate seed and grape seed-containing breads also significantly increased. Fermentation and baking process significantly influence bioactive components and antioxidant activity.