Separation efficiency is ideally controlled by molecular diffusion in capillary electrophoresis (CE). However, other adverse phenomena, such as solute adsorption on capillary surface, tend to increase the peak dispersion. An interesting alternative to limit the solute adsorption is to avoid as much as possible the contact of the solute with the capillary surface by elaborating superhydrophobic (SH) coatings on fused silica capillary surfaces. This work describes an optimized protocol to get non-wettable SH coating using hydrophobically modified silica nanoparticle suspensions (Glaco TM), based on simple capillary flushes and thermal stabilization. In this protocol, the control of the air flushing after the introduction of the Glaco TM suspension in the capillary was found crucial to get optimized coating coverage and reproducibility. The SH coating was characterized by ellipsometry, atomic force microscopy, scanning electron microscopy, contact angle (about 159°) and the observation of the meniscus of water in the coated capillary. The hydrodynamic behavior of the SH coated capillary was investigated by plotting the Poiseuille law. Finally, electrophoretic separations of a peptide mixture in acidic conditions demonstrated the interest of this approach with an increase by a factor 2 of the separation efficiency compared to fused silica capillary.