With its quality, intensity, and photoperiod, light is a decisive abiotic factor that directly influences plant biomass and the accumulation of specialized metabolites (SMs). Photosynthetically active radiation (PAR) has significant effects on primary and secondary plant metabolism and thus influences the morphological characteristics of plants and their antioxidant systems. The aim of this study was to investigate the effects of blue, red, and a 50:50 combination of blue and red LED lighting on the SM content in broccoli, mustard, and garden cress microgreens grown in an indoor farm using the zero-acreage farming technique (ZFarming). This research aims to provide valuable insights into the optimization of light spectra to improve the nutritional quality of microgreens, with a focus on sustainable and space-saving cultivation methods. After eight days, the samples were cut in the cotyledon phenophase and analyzed in a fresh state. The microgreens grown under the blue spectrum LED lighting had the highest content of ascorbic acid (112.70 mg·100 g fw⁻¹), total phenolics (412.39 mg GAE·100 g fw⁻¹), and the highest antioxidant capacity (2443.62 µmol TE·L⁻¹). The results show that the highest content of SMs in all the studied microgreens species was accumulated under the blue spectrum LED lighting. This study underlines the favorable influence of the blue spectrum (400–500 nm) on the nutrient content, especially the enhancement of SMs, in the microgreens investigated. Furthermore, the use of supplemental LED lighting proves to be a sustainable and effective means of producing microgreens with superior nutritional properties through the innovative practice of the zero-acreage farming technique.