Economic losses in a range of fruit crops due to the Drosophila suzukii (Matsumura) have become severe. Removal and treatment of fruit waste, which may harbor D. suzukii, is a key step in preventing reinfestation of fruit production. Natural fermentation for disinfesting fruit wastes from D. suzukii was examined at ambient air temperatures of 12–20 °C. Soft and stone fruit wastes infested with eggs, larvae, and pupae of Drosophila melanogaster (Meigen) or D. suzukii were placed in sealed vessels containing fruit wastes, and samples were retrieved at intervals and tested for the emergence of adults. Mean temperatures of the fruit waste in the sealed vessels during fermentation were 15–23 °C. Fermentation for 3 d was effective in disinfesting waste from different life stages of D. suzukii. Treatment for 4 d also ensured that the waste was free of viable life stages of D. melanogaster, which could be used as an indicator species for disinfestation of waste from D. suzukii owing to its greater tolerance of fermentation. The O₂ concentration of the headspace air in the vessels became undetectable after 13–16 h, with a corresponding increase in CO₂ concentration, which exceeded 80% vol/vol. The resulting hypoxia and hypercapnia may explain the efficacy of the fermentation treatment in disinfesting the waste. Fermented fruit remained attractive to D. suzukii and retained its capacity to rear a life cycle. Covering or mixing fermented fruit with a sufficient depth (0.1 m) or volume (×9) of soil or coir prevented the reinfestation of treated waste.