<p>Biostimulants have gained prominence as sustainable enhancers of plant fortification, particularly in the context of climate change. Understanding the mechanisms by which biostimulants interact with plants is essential for optimizing their application in agricultural practices. This study investigated the impact of vermicompost, a biostimulant derived from cow manure, as a seed priming agent on microgreens. Vermicompost was applied as a seed priming agent to five microgreen species: daikon, red cabbage, mustard, alfalfa, and cress. A dual phenotyping and untargeted metabolomics approach was employed to evaluate the biostimulant effect. Low-to-moderate concentrations of vermicompost (0.2–2.0&#xa0;g L^− 1) positively influenced photosynthetic efficiency, while higher concentrations (20&#xa0;g L^− 1) had a negative impact. Untargeted metabolomics revealed genotype- and dose-dependent reprogramming of secondary metabolism. Vermicompost significantly elicited the biosynthesis of nitrogen-containing compounds (glucosinolates and alkaloids), followed by that of phenylpropanoids, whereas terpenoid biosynthesis was generally downregulated. The integration of phenotypical and metabolomic data suggests multilayered correlations: (i) terpenoids and non-photochemical quenching; (ii) polyphenols and photosystem II efficiency; and (iii) electron carriers and oxidized metabolites with the ratio of photosystem II open centers, regulating the redox state of the photosynthetic apparatus. This study provides a comprehensive understanding of the biostimulant effect of vermicompost on microgreens. The findings highlight the potential of vermicompost to enhance plant fortification through its influence on photosynthetic processes and secondary metabolism. These insights contribute to the development of agricultural practices that may support more sustainable microgreen production.</p>