Food processing sustainability, as well as waste minimization, are key concerns for the modern food industry. A significant amount of waste is generated by the fruit juice industry each year. In addition to the economic losses caused by the removal of these wastes, its impact on the environment is undeniable. Therefore, researchers have focused on recovering the bioactive components from fruit juice processing, in which a great number of phytochemicals still exist in the agro-industrial wastes, to help minimize the waste burden as well as provide new sources of bioactive compounds, which are believed to be protective agents against certain diseases such as cardiovascular diseases, cancer, and diabetes. Although these wastes contain non-negligible amounts of bioactive compounds, information on the utilization of these byproducts in functional ingredient/food production and their impact on the sensory quality of food products is still scarce. In this regard, this review summarizes the most recent literature on bioactive compounds present in the wastes of apple, citrus fruits, berries, stoned fruits, melons, and tropical fruit juices, together with their extraction techniques and valorization approaches. Besides, on the one hand, examples of different current food applications with the use of these wastes are provided. On the other hand, the challenges with respect to economic, sensory, and safety issues are also discussed.