•We developed a rapid and simple technique for the provenance analysis of soybean.•Our XRF technique allows the determination of trace elements at sub-μgg−1 levels.•Concentrations of Mg, P, Cl, K, Mn, Cu, Br and Ba were used for statistical analyses.•The trace element signatures distinguished between domestic and imported soybean.•The XRF technique was also suitable for the rapid analysis of Br content in food. Trace elemental analysis of soybeans was performed using X-ray fluorescence (XRF) analysis in order to characterise the geographical origins of the beans. By optimising the measurement conditions of an energy-dispersive XRF spectrometer equipped with three-dimensional polarisation optics, determination of trace elements at the sub-μgg−1 level in soybean samples was accomplished. Forty-six samples were analysed. Results showed that there were some differences between the trace element contents, reflecting a difference in their geographical origins. A statistical analysis showed that the concentrations of eight elements (Mg, P, Cl, K, Mn, Cu, Br, and Ba) are good parameters for constructing a discriminant function for geographical origin. In conclusion, we were able to accurately distinguish between domestic and imported soybeans. The present work demonstrates that XRF is useful as a rapid and simple tool for provenance analyses of agricultural products.