Gluten is a protein group found in wheat, barley, rye, and oats, known as cereals. When this vegetable protein is introduced into the body, celiac disease can occurs. The use of bacterial and fungal oligopeptidase to ensure the cleavage of gluten into non-toxic fragments are considered a promising alternative for celiac disease. In this study, the Aspergillus niger Prolyl EndoPeptidase (AN-PEP) enzyme was cloned into pET22b vector and recombinantly produced in BL21 (DE3) pLysE cells. PEP enzyme expressed as inclusion body and was recovered by refolding. And N-terminal His-tagged recombinant protein was purified by nickel affinity chromatography. 280 mg AN-PEP enzyme from 1L bacterial culture was purified at very high yield, and this protein was 90% purity. As a result; It has been determined that the recombinantly produced PEP enzyme can digest gluten. This study shows that recombinantly produced AN-PEP (rAN-PEP) has great potential to use in the production processes of gluten-free foods.