Flavonoids and nitrogenous metabolites such as alkaloids, terpenoids, peptides and amino acids are major components of plant seeds. Conjugated forms of these compounds are soluble in water, and therefore, are easily released as chemical signals following imbibition. Once in the soil, these metabolites are first in line to serve as eco-sensing signals for suitable rhizobia and arbuscular mycorrhizal (AM) fungal partners required for the establishment of symbiotic mutualisms. They may also serve as defence molecules against pathogens and insect pests, as well as playing a role in the control of parasitic members of the family Scrophulariaceae, especially Striga, a major plant pest of cereal crops in Africa. Seed metabolites such as flavonoids, alkaloids, terpenoids, peptides and amino acids define seedling growth and, ultimately, crop yields. Thus, an improvement in our understanding of seed chemistry would permit manipulation of these molecules for effective control of pathogens, insect pests, Striga and destructive weeds, as well as for enhanced acquisition of N and P via symbioses with soil rhizobia and AM fungi.