Microbial metabolism of the stereoisomers (+)-catechin and (−)-epicatechin was compared by two analytical techniques, GC/MS for quantitative targeted analysis and GC×GC-TOF for global characterization of the metabolome, using human faecal microbiota as an inoculum of converting microbiota. The ring-fission site changed when the inocula originated from two different groups of donors, but dehydroxylation progressed similarly regardless of the inoculum. Whereas GC/MS proved to be an appropriate tool for the study of specific expected metabolites of catechin stereoisomers, GC×GC-TOF-based metabolomics analysis also revealed new metabolites not included in the targeted analyses. Quantitation and verification of identification can also be performed in a metabolomics platform, if authentic standards are available.