Coffee is one of the top selling products in the world. There are various coffee bean species around the world. Among them, Coffea Arabica is the most popular species. However, there are few studies on the metabolites of coffee beans so far. This study demonstrates effects of the planted regions on the metabolite concentrations of coffee beans. The metabolites of coffee beans can be affected by growing area even although same species are grown. Accordingly, we studied coffee bean metabolites extracted from the same species in different regions (The brand names, Kona from Hawaii, Mocha Matari from Yemen, and Blue Mountain from Jamaica) by using mixed solvent of methanol: water: chloroform. A comparative analysis by NMR spectroscopy was performed and the statistical techniques were used to figure out the differences. As a result, we found that chlorogenic acid, caffeine, citrate, and sucrose mainly contributed to the separation of the three groups. When compared with Kona and Blue Mountain, concentrations of chlorogenic acid, caffeine, and sucrose in Mocha Matari were observed to be relatively down-regulated. In addition, compared with the two other groups, concentration of citrate in Kona was observed to be up-regulated.