Fermentation is a technique applied in the food industry for preservation, processing, and novel food design. During fermentation, microorganisms generate substrate from the ingredient or source raw materials, such as enzymes, amino acids, vitamins, bioactive peptides, exopolysaccharides, organic acids, short-chain fatty acids, and phenolic compounds, among others, which have been associated with health-promoting properties. Therefore, fermented foods can be considered functional foods because they contain bioactive compounds that may improveconsumer health. To understand the development process of fermented food, metabolomics has been used. Metabolomics is an omic science currently applied in the food industry, such as food safety, food quality, and food science, in order to determine the presence of metabolite molecules smaller than 1500 Da in biological systems. In this chapter, we examine the most recent applications and advantages of metabolomics during the fermentation process and the design of fermented functional foods.