The aim of this publication is to provide up-to-date information about the recent developments in biochemical methodologies and strategies for Nigella sativa phytochemicals isolation and identification, as well as to highlight the most relevant data about its pharmacological importance in relation with its health promoting benefits actions. Because of its rich historical background, extensive researches were carried out to evidence the pharmacological effects of Nigella sativa and to explain the mechanisms behind it. Studies have shown the wide spectrum of its pharmacological effects, such as antimicrobial (especially on multiple-antibiotic resistant bacteria), nephroprotective, diuretic and antihypertensive, antidiabetic, hepatoprotective, antihyperlipidemic, anticancer activity, neuroprotective, antinociceptive, pulmonary-protective and antiasthmatic, antihistaminic, gastro-protective activity, antioxidant activity, antiinflammatory and immunomodulatory effects. The pharmacological effects are in strong correlation with the high diversity of phytochemicals (over 100 compounds). The most valuable bioactive compounds identified in Nigella sativa are thymoquinone, thymol, thymohydroquinone, retinol (vitamin A), carotenoids (β-carotene), p-cymene, carvacol, α-pinene and β-pinene, fatty acids (e.g., linoleic acid, oleic acid, palmitoleic acid, linolenic acid, myristoleic acid and others), sterols (e.g., β-sitosterol, stigmasterol, campesterol) and tocopherols (α, β, and γ). Also, Nigella sativa is a good source of minerals (calcium, phosphorus, iron, potassium, sodium, zinc, magnesium, manganese, copper, and selenium) and vitamins (vitamin A, thiamin, riboflavin, pyridoxine, niacin, folic acid, and vitamin C). The structural diversity of phytochemicals together with their health promoting benefits contributes to the high diversity of plant analysis methods like extraction, separation and detection as well as a wide variety of conditioning forms (as seeds, seed extracts, seed oil, or in different formulations, like dietary supplemental products, spices or cosmetic formulations). Also, its rich composition in bioactive compounds – together with its numerous health benefits proved over time – has contributed to the long term traditional use of Nigella sativa within traditional medicine. Taking these into account, another aim of this publication is to provide up-to-date and structured information regarding the safe use of Nigella sativa as a complementary treatment in different diseases in terms of reducing the risks and side effects of common treatments.