Current study evaluated the influence of brewers’ spent grain (BSG) flour and its three different protease-treated protein extracts (BSGPs) in the production of soybean based yogurt-alternatives (SYA). Confocal laser scanning microscopy showed that protease-treated protein extracts from BSG generated a softer, more regular and denser network distribution while BSG flour generated an irregular and less fat particle distribution. Rheological properties showed that BSG derivatives significantly (p < 0.05) increased the viscosity index of the yogurt from a range of 44–80 at the first day to a range of 91–150 at 14 days of storage showing a strengthening effect on the formed network of SYA. It also preserved the flow behavior and consistency during the storage shown by syneresis value which was stable during the 14 days storage at a range of 270–380 g/kg. BSG derivatives enhanced the amount of lactic acid on SYA which increased from 4 g/kg at control to 6–11 g/kg at SYA with BSG derivatives. In conclusion, BSG derivatives modified the microstructural properties of SYA, improved rheological behavior and acidity during the refrigerated storage.