Plants are true organic chemists—the chemical diversity of plant metabolomes goes hand in hand with functional diversity. New, often unexpected roles are being reported for both evolutionarily conserved and well-characterised central metabolites such as amino acids, nucleotides, and sugars, and for specialized/secondary metabolites such as carotenoids, glucosinolates, and terpenoids. Our review aims to highlight recent studies reporting novel roles of metabolites and to emphasize the importance of cell-wide identification of metabolite–protein complexes for the comprehensive, functional understanding of the plant metabolome.