The purpose of this study is a detailed metabolomic analysis using tandem mass spectrometry of the soybean variety Locus, selected from the collection of the Federal Scientific Center for Agrobiotechnologies of the Far East named after A. K. Chaika», to identify both the polyphenolic composition of seeds and the determination of other chemical groups in the composition of the seed. Tandem mass spectrometry studies were further supported by visual data obtained for the first time using laser microscopy. The object of the study is the seeds of the soybean variety Locus, grown in 2022 at the field site of the soybean breeding laboratory of the Federal Scientific Center for Agrobiotechnologies of the Far East named after A. K. Chaika», located in the village of Timiryazevsky (near the city of Ussuriysk). Experiments were carried out on a CLSM-800 laser confocal microscope and mass spectrometry of biologically active substances on an amaZon SL ion trap. Laser microscopy made it possible to clarify in detail the spatial distribution of the content of phenolic acids, flavonols and anthocyanins in soybean seeds. The studies were able to convincingly show that soybean polyphenolic substances and, in particular, anthocyanins are spatially localized mainly in the soybean seed coat. High-performance liquid chromatography coupled with ion trap (tandem mass spectrometry) was used to identify target analytes in soybean seed extracts. Using tandem mass spectrometry, the presence of 59 compounds was identified, of which 35 compounds represent the group of polyphenolic compounds. 15 compounds were identified for the first time in soybean extracts of the Locus variety. These are flavones: apigenin, acacetin, cirsimaritin; tetrahydroxyflavone aromadendrin 7-O-rhamnoside; lignan medioresinol; coumarin tomentin and other polyphenolic compounds. The data obtained will help intensify future research on the development and production of new drugs, dietary supplements, food additives and various functional and specialized products containing targeted soybean extracts.