Benzoxazinoids (BXDs) are a class of plant secondary metabolites that play pivotal roles in plant defense against pathogens and pests, as well as in allelopathy. This review synthesizes recent advances in our understanding of the structural and functional diversity of BXDs, the independent evolutionary trajectories of their biosynthetic pathways across different plant species, their metabolic transformations in target organisms, and the opportunities and challenges of optimizing BXD biosynthesis in crops through metabolic engineering. Compared with monocotyledons, dicotyledons employ a more diverse set of enzymes to catalyze the core reactions of BXD biosynthesis. This functional divergence—yet biochemical convergence—between monocotyledons and dicotyledons exemplifies the convergent evolution of BXD biosynthetic pathways in plants. BXDs act not only as potent antifeedants, insecticides, and antimicrobials but also function as signaling molecules that induce callose deposition and activate systemic immunity, thereby enhancing plant resistance to biotic stress. Furthermore, BXDs shape the rhizosphere by modulating microbial communities through species-specific antimicrobial activities and microbial detoxification mechanisms, ultimately exerting allelopathic effects that alter soil chemistry and nutrient dynamics. The translational potential of BXDs is increasingly recognized by synthetic biology approaches, including artificial intelligence-driven enzyme optimization, heterologous pathway engineering, and gene-editing to enhance crop resistance. Despite these promising prospects, challenges remain in balancing metabolic trade-offs and mitigating ecological risks associated with persistent accumulation of BXDs. Future research integrating multi-omics, evolutionary genomics, and microbiome studies will be essential to fully harness BXDs for sustainable crop improvement and reduced reliance on synthetic agrochemicals.