Insufficient or suboptimal dietary intake of iron (Fe) and zinc (Zn) represent a latent health issue affecting a large proportion of the global population, particularly among young children and women living in poor regions at high risk of malnutrition. Agronomic crop biofortification, which consists of increasing the accumulation of target nutrients in edible plant tissues through fertilization or other eliciting factors, has been proposed as a short-term approach to develop functional staple crops and vegetables to address micronutrient deficiency. The aim of the presented study was to evaluate the potential for biofortification of Brassicaceae microgreens through Zn and Fe enrichment. The effect of nutrient solutions supplemented with zinc sulfate (Exp-1; 0, 5, 10, 20 mg L−1) and iron sulfate (Exp-2; 0, 10, 20, 40 mg L−1) was tested on the growth, yield, and mineral concentration of arugula, red cabbage, and red mustard microgreens. Zn and Fe accumulation in all three species increased according to a quadratic model. However, significant interactions were observed between Zn or Fe level and the species examined, suggesting that the response to Zn and Fe enrichment was genotype specific. The application of Zn at 5 and 10 mg L−1 resulted in an increase in Zn concentration compared to the untreated control ranging from 75% to 281%, while solutions enriched with Fe at 10 and 20 mg L−1 increased Fe shoot concentration from 64% in arugula up to 278% in red cabbage. In conclusion, the tested Brassicaceae species grown in soilless systems are good targets to produce high quality Zn and Fe biofortified microgreens through the simple manipulation of nutrient solution composition.