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Current and previous studies on bio-based (fruit) wastes and wastewaters, with a particular emphasis on research in South Africa, were reviewed. Previous studies have focused predominantly on the beneficiation and application of fruit waste as a feedstock for renewable energy. A definite gap in knowledge and application of fruit waste streams with regard to enzyme production as a value-added product is identified. The characteristics and composition of each type of fruit waste are highlighted and their potential as feedstocks in the production of value-added products is identified. The conversion of agri-industrial wastewaters to bioenergy and value-added products is discussed, with special mention of the newly published South African Bio-Economy Strategy, and the potential production of biofuels and enzymes from waste streams using recombinant Aspergillus strains. Finally, to maximise utilisation of waste streams in South Africa and abroad, a conceptual model for an integrated system using different technologies is proposed.