Aqueous two-phase systems (ATPS) are potent, biocompatible, and cost-effective techniques for partitioning, concentration, or purification of biomolecules. In this work, the direct recovery of Bacillus subtilis D3d xylanase from the fermentation broth by the polymer-salt ATPS was optimized using response surface methodology (RSM). The 96% of xylanase recovery in the polyethylene glycol phase with the maximum purification factor (2.17 ± 0.02) and partition coefficient (69.87 ± 2.10) were the optimum responses that obtained at 9.5% (w/w) of polyethylene glycol, 20% (w/w) of sodium citrate, and pH 10. A good agreement between experimental and predicted results verified the adequacy of the RSM models. Furthermore, the efficiency of the crude and ATPS-recovered enzyme were evaluated in the biobleaching of sugar beet pulp. The ATPS-recovered enzymatic treatment of sugar beet pulp resulted in a higher release of reducing sugars (10.29 and 21.83 mg g−1) and caused 4.5% and 10% reduction in kappa number over crude-enzyme and control, respectively. This study indicated that ATPS-recovered xylanase compared to the crude enzyme has a promising application in the pulp and paper industry.