Multilayer vertical production systems using sole-source (SS) light-emitting diodes (LEDs) can be an alternative to more traditional methods of microgreens production. One significant benefit of using LEDs is the ability to select light qualities that have beneficial impacts on plant morphology and the synthesis of health-promoting phytochemicals. Therefore, the objective of this study was to quantify the impacts of SS LEDs of different light qualities and intensities on the phytochemical content of brassica (Brassica sp.) microgreens. Specifically, phytochemical measurements included 1) total anthocyanins, 2) total and individual carotenoids, 3) total and individual chlorophylls, and 4) total phenolics. Kohlrabi (Brassica oleracea var. gongylodes), mustard (Brassica juncea ‘Garnet Giant’), and mizuna (Brassica rapa var. japonica) were grown in hydroponic tray systems placed on multilayer shelves in a walk-in growth chamber. A daily light integral (DLI) of 6, 12, or 18 mol·m−2·d−1 was achieved from SS LED arrays with light ratios (percent) of red:blue 87:13 (R87:B13), red:far-red:blue 84:7:9 (R84:FR7:B9), or red:green:blue 74:18:8 (R74:G18:B8) with a total photon flux from 400 to 800 nm of 105, 210, or 315 µmol·m−2·s–1 for 16 hours, respectively. Phytochemical measurements were collected using spectrophotometry and high-performance liquid chromatography (HPLC). Regardless of light quality, total carotenoids were significantly lower under increasing light intensities for mizuna and mustard microgreens. In addition, light quality affected total integrated chlorophyll with higher values observed under the light ratio of R87:B13 compared with R84:FR7:B9 and R74:G18:B8 for kohlrabi and mustard microgreens, respectively. For kohlrabi, with increasing light intensities, the total concentration of anthocyanins was greater compared with those grown under lower light intensities. In addition, for kohlrabi, the light ratios of R87:B13 or R84:FR7:B9 produced significantly higher anthocyanin concentrations compared with the light ratio of R74:G18:B8 under a light intensity of 315 µmol·m−2·s−1. Light quality also influenced the total phenolic concentration of kohlrabi microgreens, with significantly greater levels for the light ratio of R84:FR7:B9 compared with R74:G18:B8 under a light intensity of 105 µmol·m−2·s−1. However, the impact of light intensity on total phenolic concentration of kohlrabi was not significant. The results from this study provide further insight into the selection of light qualities and intensities using SS LEDs to achieve preferred phytochemical content of brassica microgreens.