Abstract Motivation Metabolomics, as an essential tool in systems biology, is now widely accessible to researchers of all levels. Yet challenges remain in data analysis and result interpretation. To address these challenges, we introduced MetaboReport, a versatile and interactive web app that simplifies metabolomics experiment design, data preprocessing, exploration, statistical analysis, visualization, and reporting. Results MetaboReport produces a comprehensive HTML report, including project details, an introduction, interactive plots and tables, statistical results and an in-depth explanations and interpretation of the results. MetaboReport is particularly tailored for research labs and metabolomics core facilities that provide metabolomics services, allowing them to efficiently manage and document different metabolomics projects, and effectively report the metabolomics results to users. Availability and implementation MetaboReport is freely accessible on https://metaboreport.com, with source code available on GitHub (https://github.com/YonghuiDong/MetReport). Alternatively, users can install MetaboReport as a standalone desktop app (https://metaboreport.sourceforge.io).