C-13 NMR-based metabolomics was demonstrated as a useful tool for distinguishing the species and origins of green coffee bean samples of arabica and robusta from six different geographic regions. By the application of information on C-13 signal assignment, significantly different levels of 14 metabolites of green coffee beans were identified in the classifications, including sucrose, caffeine, chlorogenic acids, choline, amino acids, organic acids, and trigonelline, as captured by multivariate analytical models. These studies demonstrate that the species and geographical origin can be quickly discriminated by evaluating the major metabolites of green coffee beans quantitatively using C-13 NMR-based metabolite profiling.