Milk thistle is an alternative crop to winter cereals for southern Europe as this species is drought tolerant and its fruits contain silymarin. The aim of this study was to assess the impact of two varieties and fertilization regimes (sheep manure and inorganic fertilizer) on crop productivity. A two-factor experiment was conducted in a randomized split-plot design with three replicates. The varieties were Palaionterveno and Spata, while the fertilization treatments were control, sheep manure, and calcium ammonium nitrate applied at 75 and 125 kg N ha−1. Variety and fertilization significantly affected plants development and productivity, as well as oil and silymarin yield. The use of manure and inorganic nitrogen fertilizer increased rosette diameter, oil and silymarin yield, above-ground biomass, and fruit yield. The influence of inorganic fertilization, regardless of the application dose, was more apparent than organic fertilization. Moreover, variety significantly affected plants growth and silymarin content, as well as silymarin composition. The variety Spata had the greatest silymarin content, reaching 4.40%, and a high silybin B concentration. In conclusion, the selection of a suitable variety is important for achieving high fruit and silymarin yields, while inorganic nitrogen fertilization can maximize the productivity of the milk thistle crop.