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Facultative intracellular symbionts like the α-proteobacteria <i>Wolbachia</i> influence their insect host phenotype but little is known about how much they affect their host microbiota. Here, we quantified the impact of <i>Wolbachia</i> infection on the bacterial community of the cabbage root fly <i>Delia radicum</i> by comparing the microbiota of <i>Wolbachia</i>-free and infected adult flies of both sexes. We used high-throughput DNA sequencing (Illumina MiSeq, 16S rRNA, V5-V7 region) and performed a community and a network analysis. In both sexes, <i>Wolbachia</i> infection significantly decreased the diversity of <i>D. radicum</i> bacterial communities and modified their structure and composition by reducing abundance in some taxa but increasing it in others. Infection by <i>Wolbachia</i> was negatively correlated to 8 bacteria genera (<i>Erwinia</i> was the most impacted), and positively correlated to <i>Providencia</i> and <i>Serratia</i>. We suggest that <i>Wolbachia</i> might antagonize <i>Erwinia</i> for being entomopathogenic (and potentially intracellular), but would favor <i>Providencia</i> and <i>Serratia</i> because they might protect the host against chemical plant defenses. Although they might seem prisoners in a cell, endocellular symbionts can impact the whole microbiota of their host, hence its extended phenotype, which provides them with a way to interact with the outside world.