Compositional variation was examined across 13 microgreens species/subspecies representing Brassicaceae, Chenopodiaceae, Lamiaceae, Malvaceae and Apiaceae, grown in controlled environment. Macro-mineral concentrations were determined by ion chromatography, chlorophyll and ascorbate concentrations, and hydrophilic/lipophilic antioxidant potentials by spectrophotometry, and major carotenoids by HPLC-DAD. Nitrate hyper-accumulators and wide genotypic differences in Na, K and S concentrations were identified. Antioxidant capacity was highest in brassicaceous microgreens and significant genotypic variation was demonstrated in chlorophyll and carotenoid concentrations. High phenolic content was confirmed in Lamiaceae microgreens, with significant varietal differences, and alternative phenolics-rich microgreens from the Apiaceae were identified. Twenty-eight phenolic compounds were variably detected and quantitated through Orbitrap LC-MS/MS with flavonol glycosides, flavones and flavone glycosides, and hydroxycinnamic acids representing 67.6, 24.8 and 7.6% of the mean total phenolic content across species, respectively. The obtained information is critical for selecting new species/varieties of microgreens that may satisfy demand for both taste and health.