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In this study we developed a method for determining the geographic origin of soybeans by combining energy dispersive X-ray fluorescence spectrometry with statistical analysis. In 2018, 197 soybean samples (100 Korean domestic samples and 97 foreign samples) were collected for the construction of a geographic origin model. The mineral concentrations of 26 elements were measured and determined via the fundamental parameters approach. One-way analysis of variance, t-test, and canonical discriminant analysis were employed to reveal five elements (P, Ni, Br, Zn, and Mn) that could be used for the determination of geographic origins. The sensitivity, specificity, and efficiency for the above method were 91.0, 95.9, and 93.4%, respectively. Validation results from 60 samples collected in 2019 showed a predictive rate of 93.3% for Korean domestic soybeans and 100.0% for foreign soybeans. In conclusion, the combination of energy dispersive X-ray fluorescence spectrometry and chemometrics could be used to effectively determine the geographic origin of soybeans.