Wolbachia pipientis are maternally transmitted endosymbiotic bacteria commonly found in arthropods and nematodes. These bacteria manipulate reproduction of the host to increase their transmission using mechanisms, such as cytoplasmic incompatibility, that favor infected female offspring. Interestingly, W. pipientis infection partially rescues female fertility in flies containing hypomorph mutations of bag of marbles ( bam ) in D. melanogaster , which functions in germline stem cell (GSC) maintenance and differentiation. Here we evaluated the effect of W. pipientis variant infection on host gene expression using RNA-seq. RNA-seq analysis using the W. pipientis infected relative to uninfected bam hypomorph genotype had differential expression for many of bam’s genetic and physical interactors. The highest magnitude of differential expression of bam’s interactors and other GSC genes involved in cystoblast differentiation occurred prior to peak fertility rescue. Our analysis showed that ubiquitination and histone lysine methylation could be important mechanisms involved in the bam hypomorph fertility rescue by W. pipientis .