Biological and vegetarian raw food products, in particular based on legume sprouts, are an increasing food trend, due to their improved nutritional value when compared to seeds. Herein, protein and mineral profiles were studied in 12 lentil varieties, with varieties Du Puy, Kleine Schwarze, Rosana, Flora, Große Rote and Kleine Späths II demonstrating the highest protein percentages. After sprouting, protein percentages increased significantly in 10 of the 12 varieties, with the highest increases ranging between 20–23% in Dunkelgrün Marmorierte, Du Puy, Große Rote and Kleine Späths II varieties. While Fe concentration was significantly decreased in three varieties (Samos, Große Rote and Kleine Späths II), Zn and Mn were positively impacted by sprouting (p ≤ 0.05). Magnesium concentration was not affected by sprouting, while Ca and K had percentage increases between 41% and 58%, and 28% and 30%, respectively, in the best performing varieties (Kleine Schwarze, Dunkelgrün Marmorierte, Samos and Rosana). Regardless of the associated nutritional benefits, issues pertaining to sprouts microbiological safety must be ensured. The best results for the disinfection protocols were obtained when combining the seed treatment with SDS reagent followed by an Amukine application on the sprouts, which did not affect germination rates or sprout length. The increasing levels of sprout consumption throughout the world require efficient implementation of safety measures, as well as a knowledge-based selection for the nutritional quality of the seeds.