Polymer nanocomposites reinforced with inorganic fillers have sparked new aerospace, sports goods, automotive and civil engineering applications. Here, epoxy nanocomposites with both hydrophobic and hydrophilic silica aerogel powder fillers are presented. The use of a high porosity, mesoporous filler such as silica aerogel avoids the typical problems encountered in dispersing nanoparticles. Here, for the first time we determine the effect of silica aerogel powders and their surface chemistry, on the properties of dense epoxy-silica aerogel nanocomposites with fully infiltrated pores. The epoxy-silica interactions strongly depend on the silica surface chemistry: covalent ?Si-O-C? bonds form in the composites with hydrophilic aerogel and this leads to stronger effects on the rheological and mechanical properties, particularly at low aerogel concentration. Although, covalent bonding is mostly absent in the case of hydrophobic aerogels, the large number of Van der Waals interactions add up to a strong stabilizing effect at high aerogel loadings. The complete chemical, microstructural and mechanical characterization, from the molecular scale (NMR and FTIR) to the nanoscale (AFM-IR, Lorenz Contact Resonance, nano-thermal analysis) and microscale (SEM), offer unique insights into the toughening mechanism of mesoporous fillers. Despite the different interfacial interactions, the addition of both hydrophobic and hydrophilic silica aerogel fillers increases the fracture toughness and energy by up to 40-70% and the impact strength by up to 80-120% through a variety of mechanisms, including an increase in the fracture surface roughness, the formation of micro-shear bands, and crack front deflection.