The purpose of the research was to compare the influence of non-thermal and thermal food processing method, pulse and continuous microwave field affecting on nutrition value, selected nonnutritive components and antioxidant properties of germinated soybean seeds. Seeds of three locally grown soybean cultivars: Augusta, Aldana, Nawiko were used as the test material. The seeds were subject to germination, and then to non-thermal processing with pulse microwave field and heating by continuous microwave field. Standard AOAC methods were applied to determine basic chemical composition of samples. Trypsin inhibitor activity was determined acc. to Kakade at all method, polyphenol content was determined using Folin and Ciocalteau’s phenol phenol reagent, and antioxidant activity was measured acc. to Pekkarinen at all method using stable free radical DPPH^•. Seed germination led to statistically important (P < 0.05) reduction in trypsin inhibitor activity and polyphenol content, and it reduced antioxidant activity. Thermal processes resulted in statistically substantial (P < 0.05) inactivation of thermo-labile soybean seed component (trypsin inhibitors), and at the same time increased polyphenol content and antioxidant activity. Non-thermal process application brought about statistically considerable (P < 0.05) growth in trypsin inhibitor activity and antioxidant activity of studed seeds. Study proved positive moderate correlation between polyphenol content and antioxidant activity of germinated and put to non-thermal processing soybean seeds, and strong correlation of these parameters in case of seeds subject to thermal processes.