EMPeror is an open-source, web-based tool for visualizing high-throughput microbial community data. It allows researchers to explore 3D visualizations of microbial community data, such as principal coordinates plots, and to incorporate metadata to understand the biological factors driving these relationships. EMPeror provides features such as dynamic adjustment of data visualization, integration of metadata, and the ability to scale to thousands of data points with minimal load times. It also includes tools for displaying auxiliary data, such as biplots, procrustes analysis, and jackknifed beta diversity plots. EMPeror is designed to be user-friendly and integrates with QIIME and PyCogent. It enables interactive exploration of microbial community data, allowing users to modify visual features based on metadata. EMPeror is particularly useful for large-scale environmental sampling projects, such as the Earth Microbiome Project, and large-scale clinical projects, such as the Human Microbiome Project. The tool is available for download and is compatible with various operating systems. It is licensed under the Modified BSD license and is freely available for use. EMPeror provides a powerful and flexible tool for visualizing and analyzing microbial community data, enabling researchers to gain insights from large microbiome datasets more efficiently.EMPeror is an open-source, web-based tool for visualizing high-throughput microbial community data. It allows researchers to explore 3D visualizations of microbial community data, such as principal coordinates plots, and to incorporate metadata to understand the biological factors driving these relationships. EMPeror provides features such as dynamic adjustment of data visualization, integration of metadata, and the ability to scale to thousands of data points with minimal load times. It also includes tools for displaying auxiliary data, such as biplots, procrustes analysis, and jackknifed beta diversity plots. EMPeror is designed to be user-friendly and integrates with QIIME and PyCogent. It enables interactive exploration of microbial community data, allowing users to modify visual features based on metadata. EMPeror is particularly useful for large-scale environmental sampling projects, such as the Earth Microbiome Project, and large-scale clinical projects, such as the Human Microbiome Project. The tool is available for download and is compatible with various operating systems. It is licensed under the Modified BSD license and is freely available for use. EMPeror provides a powerful and flexible tool for visualizing and analyzing microbial community data, enabling researchers to gain insights from large microbiome datasets more efficiently.