SUMMARY: Unipept is an ecosystem of tools developed for fast metaproteomics data-analysis consisting of a web application, a set of web services (application programming interface, API) and a command-line interface (CLI). After the successful introduction of version 4 of the Unipept web application, we here introduce version 2.0 of the API and CLI. Next to the existing taxonomic analysis, version 2.0 of the API and CLI provides access to Unipept's powerful functional analysis for metaproteomics samples. The functional analysis pipeline supports retrieval of Enzyme Commission numbers, Gene Ontology terms and InterPro entries for the individual peptides in a metaproteomics sample. This paves the way for other applications and developers to integrate these new information sources into their data processing pipelines, which greatly increases insight into the functions performed by the organisms in a specific environment. Both the API and CLI have also been expanded with the ability to render interactive visualizations from a list of taxon ids. These visualizations are automatically made available on a dedicated website and can easily be shared by users. AVAILABILITY AND IMPLEMENTATION: The API is available at http://api.unipept.ugent.be. Information regarding the CLI can be found at https://unipept.ugent.be/clidocs. Both interfaces are freely available and open-source under the MIT license. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.