Polyphenols and isoflavones are the main bioactive components of soybean. During traditional processing, many active compounds are lost because of filtration and discard of okara. However, reports on changes in phenolic compounds, especially bound phenolic compounds (BPC), during the fermentation of whole soybean milk (WSM) are few. In this paper, three lactic acid bacterias (LABs) with different β-glucosidase activities were used to evaluate the effect of β-glucosidase and different okara contents in soybean milk on the conversion of extractable and non-extractable polyphenols during fermentation. The results showed that the action of β-glucosidase improved the release of BPC and isoflavones. During WSM fermentation, the β-glucosidase-producing capacity of LABs strongly correlated with both the decrease in conjugated phenolic compounds and isoflavone glycosides, and the increase in free phenolic compounds and isoflavone aglycones. With the increase of okara content, the acid tolerance of Lactobacillus delbrueckii b8 was enhanced and the viability increased. During L. delbrueckii b8-mediated fermentation, the β-glucosidase activity of soy milk with high okara content (59.07 ± 1.48 U/mL) was 1.62 times that of soy milk with low okara content (36.43 ± 1.38 U/mL). As the okara concentration increased, the release of soybean polyphenols increased. Moreover, high okara content and high β-glucosidase activity mutually promote polyphenol conversion in soy yogurt. Therefore, WSM fermentation by β-glucosidase-producing LAB is a method for increasing the phenolic compound content in soymilk. This approach can offer a theoretical guide for efficiently utilizing soybean polyphenols and developing phenolic compound-rich soymilk.