Background: The oils obtained from the seeds of Nigella sativa, also named black cumin, are rich in bioactive compounds that strengthen immunity and support human health. This study aimed to compare Nigella sativa oils pressed from Egyptian (Eg-NSSO), Ethiopian (Et-NSSO), and Syrian (Sy-NSSO) seeds. Methods: The analyzed oils were obtained from a local company. The content of phenolic compounds, tocochromanols, phytosterols, volatile compounds, triglycerides, and fatty acids composition was determined using chromatographic methods. The oxidative stability was determined by Rancimat technique as well as the determination of DPPH and ABTS scavenging activity. As an assessment of bioactivity, the antimicrobial and anti-aflatoxigenic properties of oils were evaluated. Results: Ethiopian oil had highest content of phenolic compounds, flavonoids, phytosterols, and tocochromanols and was characterized by the longest induction period (IP = 7.89 h). The share of thymoquinone was the highest in Ethiopian oil (34.84%), followed by Egyptian (27.36%), then Syrian (22.59%). Ethiopian oil recorded a high antibacterial activity, while Egyptian oil showed a unique antifungal activity against toxigenic fungi. Aflatoxins’ secretion into liquid medium containing NSSO was reduced, especially with Egyptian oil.