The manuscript describes an optimized analytical protocol for the measurement of hardness and Young’s modulus in micrometric Sol-Gel coatings for brake components. In particular, two different hybrid organic-inorganic coatings with different functional properties are presented as example. The work pays particular attention in developing and optimizing reliable hardness measurements procedures by coupling Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) and Nano-Indentation (NI) probes. In particular, FIB-SEM is used to directly assess the actual coating thickness, avoiding any eventual damaging and artifact in thin layers possibly due to classical metallographic sample preparation. Once the thickness of the investigated coating is determined, then it is used as input parameter to calculate proper indentation penetration depth and load for NI measurements, thus avoiding any influence of the substrate in the obtained results. Finally, it is demonstrated that the proposed analytical protocol provides stable, reproducible and reliable hardness measurements in thin Sol-Gel coatings.