The bovine digestive microbiota outside the rumen has been the subject of only limited research, despite its crucial role in animal health and productivity. The present study sought to provide a comprehensive meta-analysis concerning the faecal microbiota of lactating Holstein dairy cows. A systematic online search of PubMed (June 2023) was conducted to identify studies examining the faecal microbiota of lactating Holstein dairy cows using the V3-V4 hypervariable region of the 16S rRNA gene, as this region has been the subject of the most extensive research. The raw sequencing data were obtained from public repositories or provided directly by the authors. They were processed using FROGS v4.1.0 and the results were pooled by taxonomy. The statistical analysis was performed mainly using the mixOmics and microbiome R packages. The sample quality (e.g. number of sequences per sample) was found to be highly variable among the studies. A paucity of metadata was available and some authors did not share raw data. A systematic online search on PubMed retrieved 526 articles. Twenty-eight articles met the required inclusion criteria, resulting in 1,040 samples in total. As expected, samples from the same study would have a similar community structure and grouped together. The core microbiota was examined and within PCA allowed to reduce the study effect and build microbiota profiles. This meta-analysis provides an overview of the faecal microbiota of lactating Holstein dairy cows using up-to-date data. Despite the variability in sample quality and the limited access to the data, key microbial profiles and core microbiota features were identified. The observed study-dependent clustering highlights the strong influence of the environment and experimental conditions on microbial communities. The findings underscore the necessity for standardization of assessment methods and the enhancement of data sharing to facilitate the advancement of microbiota research in the future.