EMPeror is an open-source, web browser-enabled tool designed for visualizing high-throughput microbial community data. It offers a versatile command-line interface and an interactive user interface, enabling researchers to explore 3D visualizations of microbial community data, such as principal coordinates plots. Key features include the ability to visualize gradients and categorical data, adjust the size and transparency of community spheres, dynamically scale axes, and display auxiliary data like biplots and jackknifed beta diversity plots. EMPeror significantly reduces file sizes and loading times compared to existing tools, making it easier to share visualizations via email or web pages. The tool is tailored to the needs of microbial ecologists, facilitating rapid insights from large microbiome datasets. It is particularly useful for large-scale environmental and clinical projects, such as the Earth Microbiome Project and the Human Microbiome Project.EMPeror is an open-source, web browser-enabled tool designed for visualizing high-throughput microbial community data. It offers a versatile command-line interface and an interactive user interface, enabling researchers to explore 3D visualizations of microbial community data, such as principal coordinates plots. Key features include the ability to visualize gradients and categorical data, adjust the size and transparency of community spheres, dynamically scale axes, and display auxiliary data like biplots and jackknifed beta diversity plots. EMPeror significantly reduces file sizes and loading times compared to existing tools, making it easier to share visualizations via email or web pages. The tool is tailored to the needs of microbial ecologists, facilitating rapid insights from large microbiome datasets. It is particularly useful for large-scale environmental and clinical projects, such as the Earth Microbiome Project and the Human Microbiome Project.