The aim of this study was to evaluate the effect of application of two mineral selenium forms (selenite Se4+ or selenate Se6+) on the accumulation of this element by alfalfa (Medicago sativa), radish (Raphanus sativus var. sativus), and white mustard (Sinapis alba) at early stages of plant development for biofortification of sprouts with selenium, and the impact of this process on selected phytochemical traits. For this purpose, selenium-biofortified sprouts were analyzed for the contents of l-ascorbic acid and anthocyanin as well as their antioxidant activity. Additionally, the concentration of selenium in the biomass was determined. It was demonstrated that the application of selenium contributed to increased bioaccumulation of the element in the sprouts, constituting an effective method for the production of selenium-biofortified food. Selenate was accumulated less efficiently than was selenite. It was found that a concentration of 20 µmol L−1 Se in the form of both selenate and selenite was an optimal dose for enrichment of the sprouts with this element. Biofortification of the experimental species with selenium (20 µmol L−1) generally increased accumulation of anthocyanins but did not significantly alter the level of l-ascorbic acid and free radical scavenging activity. Therefore, it seems that consumption of selenium-biofortified sprouts can be an effective way to supplement low-selenium diets with this element.