Microgreens have attracted considerable scientific and commercial interest due to their phytochemical composition, nutritional value, and desirable sensory attributes. Swiss chard (Beta vulgaris L. var. cicla) and spinach (Spinacia oleracea L.) are widely cultivated and appreciated for their nutritional and phytochemical characteristics, including phenolic compounds with recognized antioxidant and health-promoting properties. However, comparative information on the phenolic profiles of these species at the microgreen stage remains limited. This study aimed to compare the phenolic profiles of Swiss chard and spinach microgreens cultivated under identical indoor conditions. Seeds were sown in vermiculite-filled trays and cultivated in a walk-in growth chamber under LED lighting, a 14/10 h light/dark photoperiod, 20–25 °C, and ~60% relative humidity. Plants were irrigated with a 3:1:6 NPK nutrient solution. Spinach and Swiss chard microgreens were harvested 14 and 17 days after sowing, respectively, and their phenolic profiles were characterized by high-performance liquid chromatography coupled with diode-array detection and electrospray ionization mass spectrometry (HPLC-DAD-ESI/MS). Flavonoids constituted the predominant phenolic class in both species. Swiss chard microgreens were characterized by the predominance of vitexin derivatives, whereas spinach microgreens exhibited a phenolic profile dominated by spinacetin and patuletin derivatives. Overall, these findings revealed distinct phenolic signatures in Swiss chard and spinach microgreens, highlighting their phytochemical diversity and relevance as dietary sources of bioactive compounds.