Glycosides are important functional materials in foods. Transformation, especially hydrolysis, of the sugar moieties tends to improve the functional properties of the administered glycosides in vivo. Various probiotic bacteria and edible food-grade fungi such as bifidobacteria, lactobacilli, leuconostocs, yeasts, and aspergilli are potential industrial microorganisms to transform glycosides of ginsenosides from ginseng, platycodin saponins from Platycodon grandiflorum, Trignoella foenum-graecum (TFG) saponins, and isoflavones from soybeans and Puerariae radix, respectively, by fermentation or enzymatic reaction. In this review, various transformation pathways bearing potential significance with respect to the changes in structure and function of the various glycosides from the food materials will be introduced. In conclusion, the proper combination of food microorganisms and transformation conditions will improve the functionality and the sensory value and reduce the cytotoxicity of the functional glycosides present in various functional food raw materials.