Objectives: The aim of this study was to compare the radiographic objectives of a novel silk fibroin (SF) nanofiber membrane to collagen membrane (CM) as a regenerative material for treating of intrabony periodontal defects using minimally invasive surgery in a prospective, randomized, single-blind, controlled study design. [ Patients and Methods: Thirty periodontal intrabony defects in thirty patients were included in the study. Patients were randomly assigned into three groups; Group 1: Minimally Invasive Surgical Technique (MIST), Group 2: MIST with CM, Group 3: MIST with Silk Fibroin (SF) nanofiber membrane. Radiographic parameters including linear, defect angulation measurements and the intrabony component fill were evaluated at baseline and six months following surgical therapy. Results: The study found a significant gain in radiographic parameters between baseline and after a 6-month follow-up period. In this study, radiographically regarding intra-bony component fill there was insignificant difference as P = 0.18, 0.44, and 0.07 regarding G1, G2, and G3 respectively.