Changes to the community of symbiotic bacteria and fungi in the brown planthopper, Nilaparvata lugens Stål, were measured at different times after exposure to conidial suspensions of Metarhizium flavoviride Gams and Roszypal. Over all concentrations tested, bacterial species associated with N. lugens comprised 8 phyla, 17 classes, 22 orders, 26 families, and 31 genera of which the relative proportions of Arsenophonus, Burkholderia, Enterobacter, Pseudomonas, Stenotrophomonas, and Bacteroides were highest. The relative abundance and diversity of bacteria were highest in the carrier control (0.05% Tween-80 only). Fungi comprised 1 phyla, 5 classes, 10 orders, 13 families, and 18 genera, with Metarhizium being the dominant taxon in specimens from all treatment groups. Metarhizium spp. was greatest in the concentrations of 107 and 108 conidia/ml at 72 hours after exposure, reaching 94.82% and 93.74% of taxonomic units, respectively. We deduced that M. flavoviride competes for nutrition with midgut microorganisms; therefore, exposure to a pathogenic fungus will change the abundance and diversity of bacterial and fungal microorganisms in the midguts of hosts, and pathogens will impact the structure of bacterial communities in the host midgut with an alteration in the bacterial species composition. We observed that following the exposure of N. lugens to M. flavoviride, Metarhizium spp. dominated in the midgut of the host, the abundance and diversity of midgut fungal microorganisms decreased, and the dominant bacterial species in the midgut shifted.