Microgreens constitute ready-to-eat functional foods, being rich sources of phytonutrients and phytochemicals. Because of their short life cycle, seed priming is a promising strategy to fortify their functional outcome. Vermicompost was applied as seed priming agent for four Brassicaceae microgreens of nutritional interest. The combination of untargeted metabolomics and in vitro assays highlighted the involvement of phenolics and glucosinolates in the functional traits of microgreens, following species-specific responses. Cress accumulated specific polyphenols at low vermicompost dosage, while daikon mainly accumulated aliphatic glucosinolates. Mustard and red cabbage were found to repress glucosinolate accumulation while eliciting polyphenols following vermicompost fortification. The application of machine learning chemometrics revealed that both families of compounds coordinated the functionality of microgreens in terms of antioxidant and neuroprotective bioactivities, highlighting the importance of optimizing genotype-specific interventions. This research sheds light on nutritional enhancement of functional foods, paving the way toward the establishment of novel sustainable food systems.