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Microgreens are edible seedlings of vegetables and flowers species which are currently considered among the five most profitable crops globally. Light-emitting diodes (LEDs) have shown great potential for plant growth, development, and synthesis of health-promoting phytochemicals with a more flexible and feasible spectral manipulation for microgreen production in indoor farms. However, research on LED lighting spectral manipulation specific to microgreen production, has shown high variability in how these edible seedlings behave regarding their light environmental conditions. Hence, developing species-specific LED light recipes for enhancement of growth and valuable functional compounds is fundamental to improve their production system. In this study, various irradiance levels and wavelengths of light spectrum produced by LEDs were investigated for their effect on growth, yield, and nutritional quality in four vegetables (chicory, green mizuna, china rose radish, and alfalfa) and two flowers (french marigold and celosia) of microgreens species. Microgreens were grown in a controlled environment using sole-source light with different photosynthetic photon flux density (110, 220, 340 µmol m−2 s−1) and two different spectra (RB: 65% red, 35% blue; RGB: 47% red, 19% green, 34% blue). At harvest, the lowest level of photosynthetically active photon flux (110 µmol m−2 s−1) reduced growth and decreased the phenolic contents in almost all species. The inclusion of green wavelengths under the highest intensity showed positive effects on phenolic accumulation. Total carotenoid content and antioxidant capacity were in general enhanced by the middle intensity, regardless of spectral combination. Thus, this study indicates that the inclusion of green light at an irradiance level of 340 µmol m−2 s−1 in the RB light environment promotes the growth (dry weight biomass) and the accumulation of bioactive phytochemicals in the majority of the microgreen species tested.