Verifying the geographical origin of soybeans (Glycine max [Linn.] Merr.) is a major challenge as there is little available information regarding non-parametric statistical origin approaches for Chinese domestic and imported soybeans. Commercially procured soybean samples from China (n = 33) and soybeans imported from Brazil (n = 90), the United States of America (n = 6), and Argentina (n = 27) were collected to characterize different producing origins using stable isotopes (δ2H, δ18O, δ15N, δ13C, and δ34S), non-metallic element content (% N, % C, and % S), and 23 mineral elements. Chemometric techniques such as principal component analysis (PCA), linear discriminant analysis (LDA), and BP–artificial neural network (BP-ANN) were applied to classify each origin profile. The feasibility of stable isotopes and elemental analysis combined with chemometrics as a discrimination tool to determine the geographical origin of soybeans was evaluated, and origin traceability models were developed. A PCA model indicated that origin discriminant separation was possible between the four soybean origins. Soybean mineral element content was found to be more indicative of origin than stable isotopes or non-metallic element contents. A comparison of two chemometric discriminant models, LDA and BP-ANN, showed both achieved an overall accuracy of 100% for testing and training sets when using a combined isotope and elemental approach. Our findings elucidate the importance of a combined approach in developing a reliable origin labeling method for domestic and imported soybeans in China.