Microgreens growing under electric (artificial) lighting in controlled environments often have short hypocotyls, which can be difficult for machine harvest. To investigate whether early-stage dark treatment can promote hypocotyl elongation without compromising microgreen yield and quality, two different seed-size species, sunflower (Helianthus annuus ‘Black oil’) and arugula (Eruca sativa ‘Rocket’), were tested. Seeds of sunflower and arugula were sown in pots, and the pots were placed inside support trays. During the first 5 days after seeding, half of the pots per species within each tray were covered with an upside-down black tray as dark treatment, and another half were kept under light. The light treatment was provided by continuous (24-h) lighting with a combination of red (85%) and blue (15%) light-emitting diodes at a photosynthetic photo flux density of around 100 μmol·m⁻²·s⁻¹. After 5 days of dark treatment, the black covers were removed and the plants were grown under the above lighting treatment till harvesting. The microgreens were harvested at 7 d and 12 d after seeding for sunflower and arugula, respectively. Early-stage dark treatment promoted hypocotyl elongation by 26% and 28% for sunflower and arugula, respectively. Microgreen yield was increased by 13% for sunflower and reduced by 24% for arugula under dark treatment. Dark treatment increased cotyledon succulence by 14% for sunflower, but reduced cotyledon size by about 25% for arugula despite increases in red color and succulence of arugula hypocotyls. For both species, cotyledon color and soluble solids content were not affected by dark treatment.