The main problem in the production of cellulosic ethanol is to ensure an efficient and cost-effective raw material pretreatment, guaranteeing a high degree of lignocellulose decomposition. Microwave radiation can be an alternative to conventional biomass heating, which in association with the use of dilute acid and a cellulolytic enzyme ensures a high degree of cellulose degradation. We evaluated the effectiveness of microwave dilute acid pretreatment of wheat and rye stillage in terms of the amount of sugars released, formation of fermentation inhibitors and their removal, and fermentation efficiency. Regardless of the type of stillage used, the highest glucose concentration after pretreatment (above 156 mg g−1 of DW) and the highest yield of cellulose hydrolysis after 24 h of the process (over 75%) were obtained using microwave power of 300 W, 15 min, 54 PSI. Fermentation of lignocellulosic hydrolysates obtained under the above-mentioned conditions ensured high ethanol concentrations of up to 20 g L−1 with full attenuation after just 48 h. Too intensive microwave treatment (152 PSI, 10 min) increased the concentration of sugar dehydration products which inhibited yeast fermentation activity and led to a lower ethanol yield. Detoxification with activated carbon reduced the toxic stress caused by the high concentration of HMF in hydrolysates. The application of microwaves is an interesting alternative to conventional barothermal methods. The possibility of an effective use of waste biomass of wheat/rye stillage for the production of cellulosic ethanol creates a prospect of integrating first and second generation ethanol production within one technological process.