Display omitted •Almost all of raffinose and stachyose were consumed by kombucha microorganisms.•Almost all of glucoside isoflavones transformed into aglycone isoflavones.•Total phenolic, ferulic acid, chlorogenic acid and vitamin C contents increased.•Antioxidant and inhibition activities to α-glucosidase and α-amylase increased. Soymilk fermentation with kombucha was perfomed at 28 °C and 37 °C, and changes in the number of microorganisms, bioactivity and chemical compositions were analyzed during fermentation. Yeast, acetic acid bacteria (AAB), and lactic acid bacteria (LAB) showed substantial growth in the soymilk, and fermentation at 37 °C and 28 °C promoted the growth of LAB and AAB, respectively. The flatulence factors of raffinose and stachyose were entirely and mostly consumed during fermentation, respectively. Nearly all the glucoside isoflavones were transformed into aglycone isoflavones by β-glucosidase hydrolysis. Total phenolic, ferulic, chlorogenic and ascorbic acid (VC) contents significantly increased after fermentation. The antioxidant and inhibition activities to α-glucosidase and α-amylase of kombucha-fermented soymilk significantly increased, and were higher at 37 °C than at 28 °C. In conclusion, fermentation with kombucha can enhance the health-promoting properties of soymilk.