In the present study, a chitosan-based, multifunctional and double-faced barrier membrane was developed for the periodontitis therapy. The porous surface of the membrane was coated with bone-like hydroxyapatite (HA) produced by microwave-assisted biomimetic method and enriched with bone morphogenetic factor 6 (BMP-6) to enhance the bioactivity of chitosan. This surface of the membrane was designed to be in contact with the hard tissue that was damaged due to periodontitis. Otherwise the nonporous surface of membrane, which is in contact with the inflammatory soft tissue, was coated with electrospun polycaprolactone (PCL) fibers to prevent the migration of epithelial cells to the defect area. PrestoBlue, Scanning Electron Microscope (SEM) and real-time PCR results demonstrated that while porous surface of the membrane was enhancing the proliferation and differentiation of MC3T3-E1 preosteoblasts, nonporous surface of membrane did not allow migration of epithelial Madine Darby Bovine Kidney (MDBK) cells. The barrier membrane developed here is biodegradable and can be easily manipulated, has osteogenic activity and inactivity for epithelial cells. Thus, by implanting this membrane to the damaged periodontal tissue, bone regeneration will take place and integrity of periodontal tissues will be preserved.