<jats:title>Significance</jats:title> <jats:p>Compound Activity Mapping provides an alternative approach to natural products drug discovery by integrating high-content biological screening and untargeted metabolomics to directly reveal the identities and biological functions of individual bioactive compounds in complex natural product libraries. This accelerated discovery pipeline addresses many of the issues that have contributed to the decline of natural products research in some areas by improving dereplication and lead prioritization strategies. The detailed structural and functional annotation offered by this tool may help to improve the integration of natural products with modern high-content, high-throughput screening and provide an additional strategy for the discovery of the next generation of natural product-inspired drug leads and chemical probes.