It is only recently that fermentation has been facing a dynamic revival in the food industry. Fermented fruit-based beverages are among the most ancient products consumed worldwide, while in recent years special research attention has been granted to assess their functionality. This review highlights the functional potential of alcoholic and non-alcoholic fermented fruit beverages in terms of chemical and nutritional profiles that impact on human health, considering the natural occurrence and enrichment of fermented fruit-based beverages in phenolic compounds, vitamins and minerals, and pro/prebiotics. The health benefits of fruit-based beverages that resulted from lactic, acetic, alcoholic, or symbiotic fermentation and specific daily recommended doses of each claimed bioactive compound were also highlighted. The latest trends on pre-fermentative methods used to optimize the extraction of bioactive compounds (maceration, decoction, and extraction assisted by supercritical fluids, microwave, ultrasound, pulsed electric fields, high pressure homogenization, or enzymes) are critically assessed. As such, optimized fermentation processes and post-fermentative operations, reviewed in an industrial scale-up, can prolong the shelf life and the quality of fermented fruit beverages.