Purpose <p>Metabolomics, a pivotal tool in systems biology, has revolutionized the study of functional beverages by enabling comprehensive profiling of their bioactive compounds and metabolic pathways. This review explores recent advancements and innovations in metabolomics applications within the realm of functional beverages, encompassing both fermented and unfermented drinks.</p> Recent Findings <p>Highlights the transformative role of metabolomics in elucidating the complex biochemical interactions that define the health-promoting properties of functional beverages. Metabolomics enables the identification and quantification of diverse metabolites such as phenolic compounds, organic acids, and vitamins, offering insights into their biosynthesis and metabolic fates during beverage processing and consumption.</p> Summary <p>Metabolomics plays a crucial role in deciphering the complex metabolic profiles of functional beverages, offering insights into their nutritional composition and functional attributes. By elucidating these complex metabolic networks, metabolomics enables targeted interventions. It also facilitates identifying and enhancing the health benefits of fermented and unfermented functional beverages. Future advancements will focus on employing advanced analytical techniques and computational methods to fully harness metabolomics for the development of next-generation functional beverages.</p>