Most fermented foods are dairy-based products; however, foods prepared using non-dairy-based materials such as grains, cereals, vegetables, and fruits can meet the dietary requirements of consumers following different food practices, including vegans and consumers that have dietary issues with dairy-based products. Traditional food fermentations have been conducted by the functioning of bacterial and yeast cultures using the inoculum of uncharacterized microorganisms isolated from naturally fermenting foods. However, pure viable strains of microorganisms characterized as probiotic cultures have the potential for their application in the fermentation process. Such fermented foods can be labeled as probiotic products, displaying the names of strains and their viable number contained in the portion size of that specific product. The significance of the development of probiotic functional food is that they can be used as a source of nutrition; in addition, their consumption helps in the recovery of healthy gut microbiota. In a fermented food, two components—the fermented substrate and the microorganism(s)—are in a synergistic relationship and contribute to healthy gut microbiota. The intake of probiotic foods for sustainability of a healthy gut can manipulate the functioning of gut–brain axis. The aim of this article is to present a review of published research conducted with specific strains characterized as probiotics, which have been studied to perform the fermentation growing on the matrices of non-dairy-based substrates.