An adequate and balanced diet is fundamental in preserving the health of astronauts from several space-induced diseases. Therefore, the integration of a diet with fresh food, rich in bioactive compounds such as microgreens produced directly onboard, may be useful in space for human nutrition. However, ionizing radiation (IR) in space represents a significant hindrance for organisms, with potential critical outcomes on plant morpho-anatomical, eco-physiological, and biochemical aspects, depending on the plant and IR features (e.g., species, developmental stage, IR dose, and type). In this study, we analyzed the effect of different doses of X-rays (0-control, 0.3, 1, 10, 20, and 30 Gy) on the morpho-anatomical and nutritional traits of microgreens of Brassica rapa L., irradiated at the stage of germinated seeds. After the irradiation, microgreens were cultivated in controlled conditions. At harvest, the morpho-biometric traits were analyzed, along with the leaf functional anatomical traits and the phytochemical content of the aboveground biomass. The results showed that X-ray exposure does not induce detrimental effects on growth, while it stimulates the production of antioxidants, improving plant defense and nutritional value. The overall results support the idea of using this species in space as a supplemental functional food.