Selenium (Se) is an essential micronutrient that plays a critical role in human health, and its deficiency has been linked to increased risks of cancer and cardiovascular diseases. Agronomic biofortification of microgreens with Se in indoor vertical farming systems offers a sustainable strategy to address this global health challenge and promote food security. This study aimed at evaluating the biofortification of white Swiss chard (Beta vulgaris subsp. cicla) microgreens, using two inorganic Se forms (sodium selenate and sodium selenite), and characterizing their phytochemical and mineral profiles. Microgreens were grown in a climate-controlled walk-in growth chamber equipped with LED lighting. Seeds were sown in polystyrene trays containing biodegradable cellulose sheets and vermiculite, and cultivated under a 14/10 h light/dark photoperiod at 20–25 °C and ~60% relative humidity. Irrigation was performed using a 3N–1P–6K nutrient solution supplemented with sodium selenate or sodium selenite at 10, 20, or 40 µM Se, as well as a mixed 20 µM treatment. Fourteen days after sowing, microgreens were harvested, and their phytochemical and mineral profiles were determined using chromatographic and spectroscopic techniques, respectively. The analysis allowed the characterization of up to 10 phenolic compounds (2 phenolic acids and 8 flavonoids), 7 betalains (2 betacyanins and 5 betaxanthins), and 17 saponins. Sodium selenite treatment resulted in higher concentrations of saponins, whereas sodium selenate led to greater phenolic compounds, betalains, and mineral accumulation. In conclusion, Se biofortification, particularly with sodium selenate, significantly improved the nutritional and functional properties of white Swiss chard microgreens grown under indoor conditions.