Insect-associated microbes exert diverse effects on host fitness. This study provides insights into the microbiota of the bamboo aphid, and their response to infection. 16S rRNA and ITS sequencing data were used to analyze the bacterial and fungal samples associated with healthy, infected, and starved aphids. At ≥97% nucleotide similarity, the total reads were clustered into 79 bacteria and 97 fungi operational Taxonomic Units (OTUs). The phyla Proteobacteria and Ascomycota dominated the bacterial and fungal communities, respectively. The significant divergence in OTU distribution presented differential profiles of the microbiota in response to host conditions. Lower α-diversity indices were found in bacterial and fungal diversity when the aphids were experiencing fungal infection and starvation stresses, respectively. The β-diversity analyses of the communities showed significant differences among the three host conditions, demonstrating that aphid-associated microbiota could significantly shift in response to varying host conditions. Moreover, some OTUs increased under fungal infection, which potentially increased aphid susceptibility. Presumably, infection contributed to this increase by causing the disintegration of host tissues other than host starvation. In conclusion, understanding the differentiation of aphid microbiota caused by fungal entomopathogens helped facilitate the development of novel pest management strategies.