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Multidrug and toxic compound extrusion (MATE) transporters are ancient proteins conserved among various kingdoms, from prokaryotes to eukaryotes. In plants, <i>MATE</i>s usually form a large family in the genome. Homologous MATE transporters have different subcellular localizations, substrate specificities, and responses to external stimuli for functional differentiations. The substrates of MATEs in plants include polyphenols, alkaloids, phytohormones, and ion chelators. The accumulation of these substrates is often associated with favorable agronomic traits such as seed and fruit colors, the balance between dormancy and germination, taste, and stress adaptability. In crops, wild germplasms and domesticated germplasms usually have contrasting agronomic traits such as seed color, seed taste, and stress tolerance. MATE transporters are involved in the regulations of these traits. In this review, we discuss the uniqueness and significance of there being such a large family of MATEs in plants, their substrate diversity that enables them to be involved in various agronomic traits, and the allelic forms and the expression patterns of <i>MATE</i> that are associated with favorable agronomic traits in domesticated crops. The understanding on the roles of MATEs in regulating favorable agronomic traits in crops will provide hints for the selection of genes for molecular breeding that improve desirable traits.