In the field of orthopedics and traumatology, polyether ether ketone (PEEK) serves a significant role as a suitable alternative to traditional metal-based implants like titanium. PEEK is being used more commonly to replace traditional dental products. For bonding with various adhesive agents and preserved teeth, the surface alteration of PEEK was investigated. The aim of this research was to understand how different types and contents of nano-sized silica (SiO2) fillers influenced the surface and mechanical properties of PEEK nanocomposites used in prosthodontics. In this work, PEEK based nanocomposites containing hydrophilic or hydrophobic nano-silica were prepared by a compression molding technique. The influence of nano-SiO2 type and content (10, 20 and 30% wt) on surface properties of the resultant nanocomposites was investigated by the use of scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), surface roughness analysis, and contact angle measurement. The crystalline structures of PEEK/SiO2 nanocomposites were examined by X-ray diffraction (XRD) spectroscopy. Mechanical properties were measured by microhardness, elastic compression modulus, and flexural strength. All nanocomposites showed increased surface roughness compared to pure PEEK. SEM images revealed that nanocomposites filled with low content hydrophobic nano-SiO2 showed uniform dispersion within the PEEK matrix. The introduction of 10 wt% of hydrophobic nano-SiO2 to the PEEK matrix improved elastic modulus, flexural strength, and microhardness, according to the findings. The addition of nano-SiO2 fillers in a higher weight percentage, over 10%, significantly damages the mechanical characteristics of the resultant nanocomposite. On the basis of the obtained results, PEEK/SiO2 nanocomposites loaded with low content hydrophobic nano-SiO2 are recommended as promising candidates for orthopedic and prosthodontics materials.