The present invention relates to the process for the recovery of conjugated isoflavones of residues and sub-products of food industries based on the use of soy and its derivatives. It also concerns of isoflavones obtained from food composition containing isoflavones and from the fungus genetically modified used in this process, Aspergillus oryzae ATCC 22786 (RIB 430). More specifically, the present invention concerns of a process of conversion of conjugated isoflavones, in the form of isoflavone malonate and acetates, in glucosylated isoflavones, which through fermentative and enzymatic processes are transformed into aglycone isoflavones. The products obtained in this process, pass to show a promising therapeutic as nutritive application as previously described, and may be used as a functional food or as a functional ingredient.