Although there have been large improvements to crop yield over time, this has not been accompanied by an increase in human nutritional wellbeing. In fact, there are worsening health crises associated with over- and under-consumption of particular food groups, resulting in negative human health outcomes. One solution to this is to utilize controlled environment agriculture to produce microgreens that have a high density of valuable Secondary Metabolites (SMs) such as antioxidants, phenolics, or pigment molecules that are associated with positive human health outcomes. However, optimal growth recipes to produce microgreens and their valuable nutritional compounds are not well known due to much species-specific variation, as well as biological tradeoffs between biomass and SM production. This is known as the growth defense hypothesis which describes how plants have a finite carbon budget from which to allocate to growth, or defensive, processes. To further research in this regard, this project used climate chambers to grow three species of Brassicaceae microgreens (kohlrabi, mustard, and radish) in highly controlled environmental conditions, where we used five Light Recipes, two fertilization levels, and two seeding density treatments. Our results showed that there were significant differences in SM production of these microgreens due to changes in incident light, as well as significant interactions between Fertilizer and Light Recipe for all SMs except Anthocyanins. For example, for all three species, the High Far-Red Light Recipe had the significantly highest Phenolic concentration, but with lower values of the other four SMs. The low-intensity 24-V high efficiency LEDs had the significantly highest Trolox Equivalent Antioxidant Capacity (TEAC) concentrations, while the High Red recipe had the highest Ferric Reducing Antioxidant Power (FRAP) and Flavonoid concentrations. For Anthocyanins, there were less clear patterns, with the No Green or High Red recipes having generally higher concentrations, but not always significantly. We did find some evidence supporting the growth-defense hypothesis, where our higher biomass values were negatively correlated with SM concentrations. We also found significant differences between the concentrations of SMs in leaves and stems for kohlrabi and mustard microgreens. Finally, we found some significant relationships between increasing Fertilizer dosage and SMs, for instance that Flavonoids and FRAP concentrations increased with Fertilizer application, while Anthocyanin decreased, and Phenolic and TEAC had little effect. In conclusion, we found that there were significant relationships for Light Recipe and Fertilizer, and oftentimes their interaction, for the accumulation of SMs in Brassicaceae microgreens, which can inform microgreen production environments.