The increased consumption of soy-based products leads to the incentive for more sustainable soybean processing and more accurate nutritional evaluation. The protein structures and aggregation states of different components vary with different soy products, but their relationship with digestibility is unclear. In order to study the digestion of soy protein in complex food matrices, four soy-based beverages were carefully prepared, including whole component soy beverage (WS), soy beverage with insoluble soybean residue removed (DO-WS), soy beverage with lipids removed (DL-WS), and soy protein isolate beverage (HSPI). During digestion, the microstructure revealed that particles of all soy beverages were reduced and more evenly distributed, but striated fibres (in WS and DL-WS) still remained after digestion. Tricine-SDS-PAGE profiles showed that after