Abstract Motivation High-resolution mass spectrometry permits simultaneous detection of thousands of different metabolites in biological samples; however, their automated annotation still presents a challenge due to the limited number of tailored computational solutions freely available to the scientific community. Results Here, we introduce ChemDistiller, a customizable engine that combines automated large-scale annotation of metabolites using tandem MS data with a compiled database containing tens of millions of compounds with pre-calculated ‘fingerprints’ and fragmentation patterns. Our tests using publicly and commercially available tandem MS spectra for reference compounds show retrievals rates comparable to or exceeding the ones obtainable by the current state-of-the-art solutions in the field while offering higher throughput, scalability and processing speed. Availability and implementation Source code freely available for download at https://bitbucket.org/iAnalytica/chemdistillerpython. Supplementary information Supplementary data are available at Bioinformatics online.