The conversion of isoflavones and anthocyanins during black soymilk processing including soaking and heating was investigated. During soaking procedure, the β-glucosidase activity, content of bioactive compounds including daidzein, genistein, delphinidin and cyanidin were significantly increased by deglycosylation reaction. After heating treatment at 90 °C for 1 h, the content of isoflavones β-glucosides including daidzin, glycitin and genistin were increased through a de-esterification reaction from malonyl-glucosides at high temperature. On the contrary, aglycone content including daidzein and genistein were no significant changed, this result indicated aglycones displayed well thermal stability. Moreover, anthocyanins including delphinidin-3-O-glucoside (D3G) and cyanidin-3-O-glucoside (C3G) were converted into delphinidin and cyanidin by glucose removal. HPLC analysis suggested that daidzein, genistein, D3G and C3G were bound with β-conglycinin and glycinin. Our results establish the conversion of bioactive components including daidzein, genistein, delphinidin and cyanidin by deglycosylation during soaking and heating progress and benefit to the production of soymilk.