Microgreens of Brassica (Crucifers) grown under novel amber and UV-A LED in controlled environments allows for selective accumulation of antioxidant phytochemicals. In this study, microgreens of B. rapa, B. juncea and R. sativus were compared for their phytochemical contents and antioxidant activities. Extracts were examined using HPLC-DAD/LC-HRMS/MS and in vitro chemical methods (total phenolic, TPC; total flavonoid, TFC; total anthocyanin, TAC; total carotenoid). Microgreens grown under various ratios of increasing amber (590 nm) and blue (450 nm)/decreasing red (655 nm) (rbaLED) resulted in no general trend to TPC and TFC, no effect to TAC and largely a dose-dependent response with TCC. Overall hydrophilic antioxidant activities (DPPH, FRAP and ORAC) did not show a clear pattern while lipophilic antioxidant activity was increased in a dose-dependent manner. Under rbaLED, malate esters of hydroxycinnamic acids predominated the pool of phenolics and sinigrin was the most accumulated among the glucosinolates. Expression of carotenoid biosynthetic genes was consistent with the accumulation of carotenoids. UV-A (325 nm, 340 nm, 365 nm, 385 nm) LED produced different responses in the microgreens. Overall trend under 340 nm did not benefit TPC and TFC; however, TAC was generally unchanged under overall lighting. TCC was generally highest under 325 nm and individual carotenoids were overall unchanged, except β-carotene increased and was consistent with CHXβ expression. Lutein was accumulated under 340 nm in PC and 385 nm in RR, and these corresponded with LYCβ expression. Glucosinolates were largely accumulated under 325/365 nm and decreased under 365 nm in PC, while GLS in RR/MO were significantly higher under 340/325 nm and in MS highest under 325 nm. Generally, phenolics were accumulated the greatest under 325 nm. Phenolics in RR, MO and MS had high affinity to 325 nm which also resulted in the highest contents, while PC phenolics had high affinity to both 325 nm and 385 nm. Overall, high-energy short wave UV-A (325 nm) accumulated TCC, GLS and phenolics, and increasing amber/blue LED dose benefitted TCC and lipophilic antioxidant activity.