Effects of fermentation on the chemical composition, mineral, total phenolic, total flavonoid, tannin, vitamin C, total carotenoid content, and antioxidant activity of “Nabag” Ziziphus spina-christi (L.) seeds were investigated. The fermentation process was carried out for 6, 12, 24, and 48 h. The fermentation significantly (p < 0.05) improved the chemical composition and mineral content of “Nabag” seeds, particularly the Ca, Fe, and Zn content. The phenolic, vitamin C, total carotenoid content, and antioxidant activity were significantly (p < 0.05) increased as a result of fermentation compared with unfermented Ziziphus spina-christi (L.) seeds. Fermentation of the seeds for 48 h resulted in the highest increase in crude fiber, Ca, Fe, Zn, and bioactive compounds. These results indicate the potential utilization of fermented “Nabag” seeds in the production and formulation of functional foods rich in crude fiber, essential minerals, and bioactive compounds.