Asymptomatic and hence untreated genital chlamydial infection can cause ascension of the pathogen, leading to severe sequels such as pelvic inflammatory disease and infertility. However, the complex interplay between the infection, the immune response, and particular the role of the vaginal microbiota is not well understood yet. We have shown that in a progesterone-dependent mouse model, genital tract abundance of C. muridarum is being reduced in an E. faecalis-associated manner. While this goes along with further changes in the urogenital environment (e.g. tissue structure, immune cell abundance), we have experimentally proven that E. faecalis is providing partial reduction of the pathogen when modulating the vaginal microbiota of the mouse. We were wondering by which mechanisms E. faecalis may provide this protective role in our model and analyzed its impact on C. muridarum in cell culture. We identified that transient co-incubation of E. faecalis with C. muridarum-infected cells delays the fusion of multiple inclusion which form at chlamydial cell entry. This homotypic fusion of multiple inclusion into one inclusion is an important mechanism for Chlamydia pathogenicity. While it is yet unknown, how E. faecalis impairs this fusion process, it may be central to how E. faecalis reduces chlamydial infection in our mouse model. Our model further underlines that experimental modulation of the vaginal microbiota may become a key in understanding bacteria-bacteria and bacteria-host interactions in prevention of sexually transmitted chlamydial infections.