The use of Nigella seeds in the food, pharmaceutical, and cosmetic fields is common, since the iniquity and the virtues of these plants are directly related to their characteristic phytochemical composition. This investigation focused on the comparative study of the botanical aspect, phenolic profile, and in vitro and in vivo biological activities of Nigella sativa L. (NS) and Nigella damascena L. (ND) seeds. The macro- and micro-morphological properties of these seeds were studied, and the key dissimilarities between them were clearly illustrated. The phytochemical contents and phenolic profiles were determined, and the in vitro antioxidant activity was assessed using four methods. The in vivo antioxidant and biochemical parameters of the blood of supplemented mice were determined. The results of the macro- and micro-structure analysis revealed differences between the two plants. Here, ND is characterized by higher phytochemical contents and the best antioxidant activities. The HPLC analysis indicated the presence of nine compounds, namely seven phenolic acids, particularly hydroxybenzoic and caffeic acids, and two flavonoids. The administration of ND extract to mice for 21 days at a concentration of 500 mg/kg allowed a substantial amelioration of plasma antioxidant properties. In addition, the extracts ameliorate blood parameters (cholesterol, triglycerides, glycemia, and urea). Furthermore, the antimicrobial activity of extracts demonstrated their effects on Staphylococcus and Aspergillus. Nigella seeds, in particular ND, expressed considerable in vitro antioxidant properties and demonstrated significant amelioration of mice blood properties. Consequently, these species can serve as a valuable source of compounds with various applications.