Abstract Background Modern mass spectrometry has revolutionized the detection and analysis of metabolites but likewise, let the data skyrocket with repositories for metabolomics data filling up with thousands of datasets. While there are many software tools for the analysis of individual experiments with a few to dozens of chromatograms, we see a demand for a contemporary software solution capable of processing and analyzing hundreds or even thousands of experiments in an integrative manner with standardized workflows. Results Here, we introduce MetHoS as an automated web-based software platform for the processing, storage and analysis of great amounts of mass spectrometry-based metabolomics data sets originating from different metabolomics studies. MetHoS is based on Big Data frameworks to enable parallel processing, distributed storage and distributed analysis of even larger data sets across clusters of computers in a highly scalable manner. It has been designed to allow the processing and analysis of any amount of experiments and samples in an integrative manner. In order to demonstrate the capabilities of MetHoS, thousands of experiments were downloaded from the MetaboLights database and used to perform a large-scale processing, storage and statistical analysis in a proof-of-concept study. Conclusions MetHoS is suitable for large-scale processing, storage and analysis of metabolomics data aiming at untargeted metabolomic analyses. It is freely available at: https://methos.cebitec.uni-bielefeld.de/. Users interested in analyzing their own data are encouraged to apply for an account.