Recently, metabolomics has grown rapidly in the fields of food and agriculture. Complex physiological changes after harvest prompted the development of a new metabolomic analytical method offering more profound insight into these changes. This review presents the feasibility of a metabolomics approach to elucidate physiological changes during ripening, senescence, and disorders. Additionally, we introduce metabolomics for the authentication of agricultural products. Confirmation of species, varieties, and geographical origin via metabolomics can be useful to tackle adulteration and certify quality.