In this study, the modification of leather surface by application of TiO2-SiO2-GLYMO (3-Glycidyloxypropyltrimethoxysilane) nanocomposite coating and plasma treatment with N-2 gas activation is investigated by using Small and Wide Angle X-ray scattering methods. The protective properties were tried to be developed with TEOS and HMDSO polymers' usage in the coating process by following and controlling nano scale structural changes. The main aim was the controls of nanoscaled surface modifications and determination of the best coating process by keeping natural structure of the leathers. These scattering methods were useful to investigate the coating effects on the PTLs (Plasma Treated Leathers)' internal structures including collagen microfibers and nanofibers which are hierarchical structures of triple helix collagen. The main purpose of the work was investigate whether the structural change in the natural form of the leather is present or not in the molecular-nanoscopic and microscopic scales after the coating and the applied physico-bio-chemical processes. On the other hand, the successful protective coatings and surface modifications were determined with SAXS analyses by controlling the shape, size and distance distributions of the appeared nanoglobular aggregations. The observations of structural changes taking place within collagen fibrils as a result of surface modification provides new insight into the nature of finishing and informs future processing developments.