The vaginal microbiome is generally dominated by Lactobacilli bacteria. However, variations exist, and in some ethnic groups a dominance of non-Lactobacilli species is more common. Lactobacilli produce various antimicrobial substances which keep growth of other bacteria in check. Bacterial vaginosis (BV) is characterized by a disturbance of the vaginal microbe balance and deficiency of Lactobacilli, giving rise to the overgrowth of certain bacteria, such as Gardnerella, Atopobium, Megasphaera, Prevotella, and Sneathia. In some countries, BV can affect over half of the women. This review discusses the advantages and challenges of the current treatment options for BV and postulates directions for future research. The article examines the use of antibiotics, their effectiveness and difficulties in obtaining long-term remission, their negative impact on the existing vaginal microbiome, the risk of antibiotic resistance and the benefits and challenges of local antibiotic applications. Following this, the authors discussed the use of prebiotics and probiotics, possible reasons why clinical trials in the past showed mixed results, and what strains may be of particular importance in vaginal health, with L. crispatus and L. iners being of particular interest here. Considered are also factors that influence and enhance bacterial colonization. Lastly, the article summarizes some current thinking on Vaginal Microbiome Transplantation, which is the transfer of vaginal microbes and fluids from a healthy donor, what benefits they may have, the associated safety risks and legislative challenges. This review is a comprehensive summary of BV treatment options, their current evidence, efficacy and drawbacks, yielding useful information to consider in the clinical management of BV.