Surface morphology significantly influences the fatigue life of the metallic materials. Therefore, an improvement in surface performance is important for economic and safety applications. Silica-based coatings are anticipated to protect the metallic substrates under synergistic operating conditions, such as fatigue and corrosion. However, pure inorganic silica-based coatings are brittle and failed to bring protection to metallic substrates. The properties of the sol-gel coatings can be determined by optimizing synthesis factors, such as synthesis steps, precursors, solvents, and catalysts. Two different types of organically modified silica-based sol-gel coatings were synthesised and their mechanical response and fracture mechanics in coating to monotonic loading have been compared to pure inorganic silica sol-gel coating. It was evident that adding the organic moieties to the inorganic structure of silica sol-gel coating, increased plasticity. Therefore, this organically modified silica coating with the least brittle mechanical behavior could increase the fatigue life and corrosion resistance especially in the very high cycle fatigue (VHCF) regime, where the fatigue life is controlled by crack initiation phase. In this study, the interrupted tensile tests on coated AISI 904 L tensile specimens were followed by close SEM and FIB-cut investigations to track the fracture mechanism in the coatings and later connect the results to the cyclic investigations of chosen organically modified sol-gel coating on specimens from AISI 904L. Most importantly, the effect of surface morphology on fatigue behavior of austenitic stainless steel with application of organically modified silica-based coating in VHCF range was investigated.