Polymer/silica (PS) nanocomposites are, among numerous combinations of inorganic/organic nanocomposites, one of the most important materials reported in the literature and have been employed in a wide variety of applications. Due to this great interest in the scientific and industry community, knowledge about their physiochemistry allows for a better understanding of their development and improvement. One area of interest found in biopolymers is silica, where silica nanoparticles can be used to increase their mechanical properties and give them higher opportunities to replace synthetic plastics. With this aim in mind, molecular dynamics (MD) simulations were used to predict the structure and mechanical properties of the interphase region and nanocomposite systems of polycaprolactone (PCL), a common poly(hydroxy acid) type biopolymer, reinforced with silica nanoparticles. Two types of nanoparticles were studied to assess the effect of PEGylation: hydroxyl (ungrafted) and polyethylene glycol (PEG) (grafted or PEGylated) functionalized silica. The interaction energy between the nanoparticle and the polymeric matrix was determined, showing an increase of the affinity between each component due to the PEGylation of the nanoparticle. Through the analysis of polymer density profiles, the structure and thickness of the interphase region were determined, and it was observed that PEGylation increased the interphase thickness from 10.80 Å to 13.04 Å while it decreased the peak and average polymer density of the interphase region. Using compressed and expanded molecular models of the neat PCL polymer, the mechanical properties of the interphase region were related to its density through an interpolation model, and mechanical property profiles were obtained, from which the average values of the Young's modulus, Poisson's ratio and shear modulus of the interphase region were calculated. Finally, the mechanical properties of the nanocomposites were determined by molecular mechanics simulations, showing that the silica nanoparticles increased the stiffness of the composite system to about 7-8% with respect to that of the neat polymer, having a 2.09% weight of bare silica or 2.82% weight of PEGylated silica. PEGylation did not show an additional effect on the overall mechanical properties. A mean field micromechanics model (Mori-Tanaka) corroborated the properties calculated for the interphase region using MD simulations. It was concluded that the PEGylation of the nanoparticle improved the affinity, and thus the dispersion, of the silica nanoparticles towards the PCL matrix, but with no further increase in the mechanical properties of the composite.