The overarching aim of microbiome analysis is to uncover the links between microbial phylogeny and function in order to access ecosystem functioning. This can be done using several experimental strategies targeting different biomolecules, including DNA (metagenomics), RNA (metatranscriptomics) and proteins (metaproteomics). Despite the importance of linking microbial function to phylogeny there are currently no visualisation tools that effectively integrate this information. Chordomics is a Shiny-based application for linked -omics data analysis, allowing users to visualise microbial function and phylogeny on a single plot and compare datasets across time and environments.