The article introduces QIIME 2, a reengineered and rewritten system designed to facilitate reproducible and modular analysis of microbiome data. QIIME 2 is built on a plugin architecture that allows third-party contributions, supporting advanced tools for sequence quality control, taxonomy assignment, and phylogenetic insertion. It also offers interactive visualization tools, a decentralized data-provenance tracking system, and support for multi-omics analysis. QIIME 2 aims to be a versatile and extensible platform for microbiome data science, enabling researchers to explore diverse microbiome features and advance the field of microbiome research. The article highlights the interoperability of QIIME 2 with other open-source tools and its commitment to reproducibility, transparency, and user-friendly interfaces.The article introduces QIIME 2, a reengineered and rewritten system designed to facilitate reproducible and modular analysis of microbiome data. QIIME 2 is built on a plugin architecture that allows third-party contributions, supporting advanced tools for sequence quality control, taxonomy assignment, and phylogenetic insertion. It also offers interactive visualization tools, a decentralized data-provenance tracking system, and support for multi-omics analysis. QIIME 2 aims to be a versatile and extensible platform for microbiome data science, enabling researchers to explore diverse microbiome features and advance the field of microbiome research. The article highlights the interoperability of QIIME 2 with other open-source tools and its commitment to reproducibility, transparency, and user-friendly interfaces.