Food industry effluents represent one of the major concerns when it comes to environmental impact; hence, their valorization through different chemical and biological routes has been suggested as a possible solution. The vast amount of organic and inorganic nutrients present in food industry effluents makes them suitable substrates for microbial growth. This study suggests two valorization routes for whey as dairy industry effluent and flotation wastewater from the wine industry through microbial conversion to biocontrol agents as value-added products. Cultivations of the biocontrol strain Bacillus sp. BioSol021 were performed in a 16 L bioreactor to monitor the bioprocess course and investigate bioprocess kinetics in terms of microbial growth, sugar substrate consumption and surfactin synthesis, as an antimicrobial lipopeptide. The produced biocontrol agents showed high levels of biocontrol activity against mycotoxigenic strains of Aspergillus flavus, followed by a significant reduction of sugar load of the investigated effluents by the producing microorganisms. With proven high potential of whey and winery flotation wastewater to be used as substrates for microbial growth, this study provides grounds for further optimization of the suggested valorization routes, mostly in terms of bioprocess conditions to achieve maximal techno-economical feasibility, energy saving and maximal reduction of effluents’ organic and inorganic burden.