The fungus Trichoderma reesei is a major producer of plant cell wall-degrading enzymes, such as cellulases and hemicellulases. These enzymes have been used to hydrolyze agro-industrial wastes in processes of second-generation biofuel production. The disaccharide lactose, the main byproduct of dairy industry, is considered the most attractive substrate for the commercial production of cellulases by T. reesei. In the present work, it was shown that T. reesei, cultivated in media supplemented with either lactose or galactose, secrete proteins which behave as multi-enzymatic complexes. Blue Native electrophoresis (BN-PAGE) displayed two major bands which were specific or present in higher amounts in each secretome sample, complex I in galactose medium and complex II in lactose medium. The protein components of complexes I and II were identified by means of LC-MS/MS. The complexes were composed of different glycosyl hydrolases and predicted proteins related to biopolymer metabolism. Zymography coupled to BN-PAGE showed that T. reesei secretome presents higher cellulolytic and xylanolytic activities in lactose than in galactose-induced medium. The results presented here corroborate the existence of hydrolysis based on multi-enzymatic complexes in T. reesei secretome, as observed previously in other fungi, such as Trichoderma harzianum and Penicillium purpurogenum.