Xylooligosaccharides (XOS) are components of hemicellulose and can be found in wheat bran, and barley hulls. Structurally, XOS consist of two to six xylose residues linked by β-(1,4) bonds. This makes them susceptible to subsequent treatment by intestinal bacteria, but the concentration of XOS is too low to show any prebiotic effects. Some industrial wastes, including brewers’ spent grain (BSG) and wheat bran peels (WBP), represent a major source of xylan, from which XOS is produced to provide a prebiotic effect in populations of colonic commensal microbiota. WBPs and BSGs were treated by microwave and enzymatic hydrolysis. Using the designed microwave pretreated enzymatic hydrolysis, 5.4 g of dry XOS was produced from 50 g WBP powder and 3.6 g dry XOS was produced from 50 g BSG powder. A single microwave treatment on WBP and BSG before enzymatic hydrolysis and 0.25 g/100 g enzyme raw material ratio were determined to be optimal. Effective microwave-assisted enzymatic hydrolysis of WBP and BSG were investigated, and contribute to improving the effectiveness of xylanase on WBP and BSG. Microwave-assisted enzymatic hydrolysis with xylanase and purification, obtaining food-grade XOS, was demonstrated as a step toward industrial-scale production.