There is emerging interest in the female genital tract (FGT) microbiota’s role in health and disease. It has been suggested that the FGT microbiota may play a role in the development of gynaecological cancers, which raises the question of whether microbiota manipulation could be a tool for prevention. There is a wealth of data associating HPV infection and subsequent cervical dysplasia with a high-diversity microbiome deplete of Lactobacillus species. Studies of microbiota alterations in endometrial, ovarian, vulval and vaginal malignancies are now emerging and point towards the involvement of similar pathogenic anaerobes. Whilst there are plausible mechanisms through which the microbiota can promote neoplastic transformation, it remains unclear whether the microbiota or the disease are the drivers of those changes. A number of pre-, probiotics and other non-clinician prescribed agents have claimed a therapeutic role in cervical disease. Although some document some benefit, the studies are small, of varying design and high-quality evidence to support their use is lacking. Currently no studies have examined these therapeutics in other gynaecological malignancies. Microbiome manipulation for gynaecological cancer prevention remains a welcome prospect, and warrants larger, well-designed studies. However, at present, there is insufficient evidence to support clinical recommendations that promote their use.