Metabox 2.0 is an updated version of the R package Metabox, released in 2016. The tool includes several methods for data processing, statistical analysis, biomarker analysis, integrative analysis and data interpretation. Metabox 2.0 supports a wide range of users, from bench biologists to experienced bioinformaticians. It comes with an intuitive web interface for simple data analysis. We recommend the R command line version for custom pipelines and other exclusive projects.