Miscarriage, the loss of a pregnancy before viability, can be sporadic or recurrent. Emerging evidence links miscarriage to specific microbiota compositions within the female reproductive tract (FRT). This systematic review aims to synthesise evidence on the association between sporadic and recurrent miscarriage and FRT microbiota composition, as assessed using metataxonomic profiling approaches. A systematic analysis of the 43 included studies, sampling the vaginal, cervical and endometrial microbiota supported an association between reduced Lactobacillus abundance and miscarriage, making it a potential target for therapeutic intervention. However, consistent changes in alpha and beta diversity were not observed and there was a lack of reproducibility for other compositional changes. This review also highlighted concerns about the significant bias introduced due to methodological variations and emphasises the need for future standardisation of microbial sampling, sequencing, and reporting to allow accurate comparison of results and to reduce research waste.