Fermented foods are popular around the globe for their health-promoting components and activity. In recent years, for promoting better health and nutrition, fortification and supplementation of fermented fruits are used as functional healthy beverage, especially for those who are intolerant to lactose-based products. Moreover, industrial revolution has transformed traditional fermentation process to a controlled process suitable for industrial scale production of functional ingredients. The aim of this systematic review is to provide an in-depth perspective of non-alcoholic fermented fruit beverages with an emphasis on improving bioactive and nutritional compounds such as phenolic compounds, vitamins, and minerals, and their effort as pro/prebiotics diets. For instance, consumption of fermented fruits and fruit-based probiotic foods such as kombucha has increased, and the evidence for effects on antioxidant and bioactive compounds is presented and discussed. Researchers use cutting-edge technology and innovations to convert fermented fruits into functional beverages with bioactive metabolites and phytochemicals. Hence, for the production of any functional beverage, it is essential to optimize the microbial strains that can utilize different fruit matrices as a single or in combination. These perspectives articulate fruit-based probiotics as one of the possibilities of processing fruit for culinary and pro-health purposes. Novelty impact statement: This systematic review noticeably focuses on the fruit fermentation along with various bioactive ingredients derived from fermented fruits. In addition, comprehensive description on fruits and fruit juices as a promising carrier of probiotics, fermented fruits as dietary supplements that are in the market, and related future perspectives are discussed. © 2022 Wiley Periodicals LLC.