Abstract The conventional alkaline aqueous extraction is not effective in promoting maximum protein yield from soybean meal (SBM). In this study, the steam flash-explosion (SFE) treatment was firstly employed to significantly improve the protein yield, while the protein content of soy protein isolate (SPI) decreased, concomitant with increase in carbon content of SPI. The SFE treatment led to the dissociation of insoluble protein aggregates in SBM, with subsequent increase of soluble protein aggregates formed via on-disulfide covalent bonds. The covalent coupling of the carbohydrate to the protein during SFE treatment can contribute to the dissolubility of protein and the formation of protein aggregates. After SFE treatment, surface hydrophobicity of SPI was decreased, however the emulsifying properties were improved. The emulsifying activity index and emulsifying stability index were improved to 41.94 m2/g and 35.27 min under 1.3 MPa, 180 s treatment condition. It indicated that compared to surface hydrophobicity, changes of other aspects of protein structure including the covalent coupling of carbohydrate to protein were the predominant factors that ruled the emulsifying property of protein. Industrial relevance The steam flash-explosion treatment (SFE) is an eco-friendly, low-energy and non-traditional technology, which could be performed on a large scale for the industry. The SFE treatment can effectively change the physicochemical properties of protein resulting in significant increase of protein yield and improvement in emulsifying properties of protein. After SFE treatment, the protein from heat-denatured soybean meal can be refunctionalized for application in food industry.