Microgreens have immense potential for improving dietary patterns, but little information is available regarding their overall nutritional value. We evaluated the nutritional traits of three hydroponically grown Brassica microgreens by using a Nutrient Quality Score. Micro cauliflower, micro broccoli and micro broccoli raab were grown using nutrient solutions with three different NH4:NO3 molar ratios (5:95, 15:85, and 25:75). Protein, dietary fiber, β-carotene, α-tocopherol and mineral elements (Ca, K, Mg, Fe, Zn, Cu, Mn, and Na) were analyzed. We developed the Nutrient Quality Score (NQS 11.1) on the basis of 11 desirable nutrients and 1 nutrient (sodium) to be limited. All Brassica microgreens are an excellent source of Vitamins A and E (more than 20% of the daily reference value—DRV), as well as a good source of calcium and manganese (10–19% of the DRV). Micro cauliflower showed a NQS 11.1 at 47% higher than micro broccoli raab and micro broccoli. Using NH4:NO3 25:75 molar ratio, the average score was 27% higher than other molar ratios. In all cases, the microgreens in the present study showed a higher NQS 11.1 than their mature counterpart (on the basis of data from the United States Department of Agriculture), highlighting that the score of micro cauliflower was about six-fold higher than mature cauliflower. In conclusion, the NQS 11.1 was useful for assessing the overall nutritional quality of the three Brassica microgreens, instead of simply quantifying nutrient content, in order to compare a single nutrient among different genotypes. Furthermore, the results highlight that the micro broccoli raab, micro broccoli and micro cauliflower in this study can be considered nutrient-rich vegetables that are able to improve dietary patterns more effectively than their mature counterparts.