Fusarium wilt disease in melon (Cucumis melo L.) is widespread, responsible for serious economic losses.Pot and field experiments were performed to investigate the effects of different bio-organic fertilizers(BIOs) made from organic fertilizer and different antagonistic microbes. BIOs decreased the incidence offusarium wilt disease and increased melon yield. The disease incidence of treatments with double application(BIOs applied both in the nursery and in the pot soil) was 20%, much lower than control (80%).Moreover, double application of a mix termed BIOII resulted in a 17.4-fold increase in plant fresh weightcompared to control. Application of BIOs strongly reduced the number of pathogen colony-formingunits (cfu) in stems and roots of melon. Pathogen populations were 2.27×103 and 6.67×103 cfu g−1 FW(fresh weight) on BIOII-treated stems and roots, respectively, and 8.17×104 and 3.67×104 cfu g−1 FWon control stems and roots, respectively; i.e., cfus were reduced by 97% and 82%, respectively. Microbialcommunity structure was ameliorated by all BIOs. The number of bacteria and actinomycota in rhizospheresoil increased markedly under all BIO applications compared to control. In contrast, pathogenand fungal density was dramatically higher in the rhizosphere of control plants. The activities of defenseenzymes in the leaves of melons receiving double application of BIOII were lower than those of controlplants. The highest melon yield was achieved by plants that received a double application of BIOIIin field experiments (7225 kg ha−1 vs. 4447 kg ha−1 for control plants). In conclusion, the most effectivetreatment was double application of BIOII, which minimized the incidence of wilt disease, maximizedbiomass production, and altered microbial community structure.