Implementation of cheap and eco-friendly biomass pre-treatment processes is necessary to develop sustainable bio refineries. In nature, white-rot basidiomycetes are able to degrade lignin efficiently and selectively and are thus of great interest in such bioprocesses. In this study, five basidiomycetes strains were evaluated for their ability to pretreat wheat straw under solid state fermentation. Fungal pre-treatments were carried out in glass-column reactors under operating conditions approaching industrial practices. The pre-treatment efficiency was evaluated through the quantification of dry weight losses and subsequent hydrolysis of the carbohydrate fraction by enzymatic cocktails. The highest lignin to cellulose losses ratio was obtained using a strain of Polyporus brumalis which exhibited high ligninolytic capabilities. This selectivity along with the low dry weight loss makes the pre-treatment profitable by enhancing cellulose and hemicellulose conversion yields. Therefore P. brumalis can be viewed as a promising strain to pretreat lignocellulosic biomass for bio refinery applications.