The impact of selenium (Se) enrichment on bioactive compounds and sugars and Se speciation was assessed on different microgreens (green pea, red radish, and alfalfa). Sodium selenite and sodium selenate at a total concentration of 20 μM (1:1) lead to a noticeable Se biofortification (40−90 mg Se kg −1 DW). In green pea and alfalfa, Se did not negatively impact phenolics and antioxidant capacity, while in red radish, a significant decrease was found. Regarding photosynthetic parameters, Se notably increased the level of chlorophylls and carotenoids in green pea, decreased chlorophyll levels in alfalfa, and had no effect on red radish. Se treatment significantly increased sugar levels in green pea and alfalfa but not in red radish. Red radish had the highest Se amino acid content (59%), followed by alfalfa (34%) and green pea (28%). These findings suggest that Se-biofortified microgreens have the potential as functional foods to improve Se intake in humans.