Advances in industrial biotechnology offer potential opportunities for economic utilization of agro-industrial residues such as sugarcane bagasse, which is the major by-product of the sugarcane industry. Due to its abundant availability and despite the complex chemical composition, it can be considered an ideal substrate for microbial processes for the production of value-added products. In the present study we evaluated the enzymatic production of xylooligosaccharides (XOS) and antioxidant compounds from sugarcane bagasse using XynZ from Clostridium thermocellum, a naturally chimeric enzyme comprising activities of xylanase and feruloyl esterase along with a carbohydrate binding module (CBM6). In order to reveal the biotechnological potential of XynZ, the XOS released after enzymatic hydrolysis using different substrates were characterized by capillary electrophoresis and quantified by high performance anion exchange chromatography. In parallel, the antioxidant capacity related to the release of phenolic compounds was also determined. The results indicated noteworthy differences regarding the amount of XOS and antioxidant phenolic compounds produced, as well as the XOS profile, functions of the pre-treatment method employed. The ability of XynZ to simultaneously produce xylooligosaccharides, natural probiotics, phenolic compounds and antioxidant molecules from natural substrates such as sugarcane bagasse demonstrated the biotechnological potential of this enzyme. Production of value-added products from agro-industrial residues is of great interest not only for advancement in the biofuel field, but also for pharmaceutical and food industries.