<p>Soybeans contain nutrients that must be preserved and antinutritional factors that must be inactivated. Various treatment methods for soybeans have benefits as well insufficiently studied problems. The purpose of this paper is to study the effect of infrared, autoclaving and microwave treatment on the Dongsheng 22 and <i>Glycine max</i> L. soybeans. Microwave treatment cracked the soybeans and increased seed volume by 11–20%. Infrared heating increased seed volume by 9–17%; autoclaving repeated the data for raw seed volume. There were no significant differences in crude protein, fat, ash and fiber content of soybeans across all treatments. After infrared, reduction in total starch was 10–16%, after autoclaving and microwave treatment—15–17%. Treatments had no significant effect on total phenolic content. Flavonoid content was increased by autoclaving and infrared heating by 7–9%, by microwave treatment—16%. No changes in antioxidant activity were observed during infrared heating and autoclaving of soybeans, but with microwave treatment it increased by 3–5%. Trypsin inhibitor activity during microwave treatment was reduced by 80%, and during infrared treatment and autoclaving—73–79%. Tannins were reduced by microwave treatment by 10%, and by infrared heating and autoclaving—7–9%. Reduction in phytic acid was repeated across all treatments by 43–45%. Treatments showed significant (p ≤ 0.05) preservation of nutrients and the simultaneous reduction of antinutrients in both varieties of soybeans. Milder temperature and higher heating rate are advantages of microwave treatment.</p>