Nigella sativa L. has been recognized as one of the most important medicinal plants in many parts of the world for centuries. The purpose of the current study was to evaluate the effects of fertilization and plant density on nitrogen uptake, utilization efficiency, and productivity of N. sativa under Mediterranean conditions. The three-year experiment was set up in a split-plot design with three replications. There were 2 plant densities; 200 and 300 plants m−2 with 4 fertilization levels: control, seaweed compost, farmyard manure and inorganic fertilizer. The highest seed yield (749–840 kg ha−1) was found in plants subjected to low-density and inorganic fertilization. The seed nitrogen (N) uptake as well as the nitrogen harvest index (NHI) were positively affected by the increase of available nitrogen and negatively by the increase of plant density, with their highest values recorded in the low-density and inorganic fertilization. In conclusion, plant densities greater than 200 plants m−2 result in higher crop growth but lower seed yield and decreased nitrogen uptake and use efficiency in N. sativa seeds, whereas the application of inorganic fertilizers increases crop yield, nitrogen uptake, and utilization efficiency because these fertilizers present higher nitrogen levels with higher solubility and thus faster availability for the crop in comparison with organic fertilizers.