Soil microorganisms play an important role in regulating the responses of plants to disease, but little is known regarding the role of the microbial community in rhizosphere soil in the response to diseases in papaya. To clarify how the abundance and composition of the microbial rhizosphere community of papaya change with viral infection, papaya plants resistant and susceptible to papaya ringspot virus (PRSV) were inoculated with PRSV in the field, and differences in rhizosphere soil microbial communities between healthy and susceptible papaya were analyzed. The physiochemical properties of the soil surrounding the root system were strongly affected by microbial taxa, but this did not have a significant effect on plant health. 16S rRNA and ITS sequencing revealed that disease stress increased the microbial diversity of bacteria and decreased the diversity of fungi. The analysis of soil microbial community shows that the abundance of Nitrospirae was significantly higher in HN soil (1.35 ± 0.41) than in NC soil (0.83 ± 0.13) and YK soil (0.79 ± 0.27); the abundance of Paenibacillus was higher in HN soil (0.83 ± 0.38) than in NC (0.35 ± 0.12）and YK soil (0.58 ± 0.19); the abundance of Acremonium was higher in HN soil (0.71 ± 0.37) than in NC soil (0.21 ± 0.18) and YK soil (0.48 ± 0.43). Nitrospira, Paenibacillus, and Acremonium were all beneficial microorganisms, and they were significantly higher in healthy papaya soil than in susceptible papaya soil may help viral resistance. We show for the first time that a non-soil-borne disease may influence the microbiomes of papaya rhizosphere soil. When resistant papaya was infected with PRSV, beneficial microorganisms could be recruited in the rhizosphere soil to resist viral infection. Although these results are only preliminary insights into the potential role of beneficial microorganisms in supporting plant health under viral stress, our research provides new insights with implications for the prevention and control of papaya ringspot disease, furthermore, microorganisms that promote viral resistance could expediate the development of biopharmaceuticals or green fertilizers.