One of the key elements influencing the efficiency of cellulosic ethanol production is the effective pretreatment of lignocellulosic biomass. The aim of the study was to evaluate the effect of microwave-assisted pretreatment of wheat stillage in the presence of sodium cumene sulphonate (NaCS) hydrotrope used for the production of second-generation bioethanol. As a result of microwave pretreatment, the composition of the wheat stillage biomass changed significantly when compared with the raw material used, before treatment. Microwave-assisted pretreatment with NaCS effectively reduced the lignin content and hemicellulose, making cellulose the dominant component of biomass, which accounted for 42.91 ± 0.10%. In post pretreatment, changes in biomass composition were also visible on FTIR spectra. The peaks of functional groups and bonds characteristic of lignins (C–O vibration in the syringyl ring, asymmetric bending in CH3, and aromatic skeleton C–C stretching) decreased. The pretreatment of the analyzed lignocellulosic raw material with NaCS resulted in the complete conversion of glucose to ethanol after 48 h of the process, with yield (in relation to the theoretical one) of above 91%. The highest observed concentration of ethanol, 23.57 ± 0.10 g/L, indicated the high effectiveness of the method used for the pretreatment of wheat stillage that did not require additional nutrient supplementation.