Microbiome research is driven Big Data, and access to studies’ genetic data and metadata are necessary for innovation and re-use. Sadly, many microbiome studies suffer from poor data accessibility and metadata interoperability, hampering scientific advancement. MiShMASh meets open research data (ORD) gaps in the microbiome field with a two-pronged solution in 1) a tier-based data reporting standard, and 2) open-source software to assess adherence to said standard. This resource enables users to assess how well microbiome studies meet data reporting standards prior to publication or meta-analysis. Not only does MiShMASh benefit individual researchers, but it also offers a metric for journals and funding agencies to evaluate the openness of publications. MiShMASh is a first step to the wider microbiome community’s adoption of reproducible data sharing practices, and we hope this will spark conversation for further development. The tools and guidelines developed here will improve sequence data and metadata reporting practices for greater accessibility, interoperability, and future re-use.