We report the robustness of silica hydride stationary phase, aqueous normal phase (ANP) chromatography to the chemical complexity of the intracellular metabolomes of Staphylococcus aureus and Enterococcus faecium. We specifically demonstrate that the chromatographic behavior of known metabolites is unaffected by the intracellular chemical matrix of these microbes and that this method enables untargeted profiling of their intracellular metabolites using accurate mass-retention time (AMRT) identifiers. We further demonstrate the ability of AMRT-based metabolite profiling to differentiate bacteria along genetic and phenotypic lines. Overall, these data commend the utility of ANP-based chromatography for untargeted metabolomics-based studies of microbial physiology and antibiotic resistance.