Caffeine is metabolized through various pathways in the human body, with the primary two steps yielding isomeric products. Distinguishing these metabolites is crucial for mass spectrometry-based metabolomics, for example, to assess specific drug interactions. Here, we investigate the gas-phase structures of caffeine and its metabolites─theophylline, theobromine, paraxanthine, 1-methylxanthine, 3-methylxanthine, and 7-methylxanthine─in their respective protonated ions using cryogenic gas-phase infrared spectroscopy, supported by density functional theory. The analytes exhibit varying preferences for protonation and tautomerism, particularly N9 protonation and, where applicable, a tendency for N3O2 and N1O2 amide–imidic acid and N7N9 imine–imine tautomerism. We further demonstrate that the two isomeric sets of caffeine metabolites can easily be distinguished with gas-phase IR spectroscopy, paving the way for robust identification of such molecules in metabolomics using hyphenated gas-phase techniques.