Polymer nanocomposites (NCs) offer outstanding potential for dielectric applications including insulation materials. The large interfacial area introduced by the nanoscale fillers plays a major role in improving the dielectric properties of NCs. Therefore, an effort to tailor the properties of these interfaces can lead to substantial improvement of the material’s macroscopic dielectric response. Grafting electrically active functional groups to the surface of nanoparticles (NPs) in a controlled manner can yield reproducible alterations in charge trapping and transport as well as space charge phenomena in nanodielectrics. In the present study, fumed silica NPs are surface modified with polyurea from phenyl diisocyanate (PDIC) and ethylenediamine (ED) via molecular layer deposition (MLD) in a fluidized bed. The modified NPs are then incorporated into a polymer blend based on polypropylene (PP)/ethylene-octene-copolymer (EOC), and their morphological and dielectric properties are investigated. We demonstrate the alterations in the electronic structure of silica upon depositing urea units using density functional theory (DFT) calculations. Subsequently, the effect of urea functionalization on the dielectric properties of NCs is studied using thermally stimulated depolarization current (TSDC) and broadband dielectric spectroscopy (BDS) methods. The DFT calculations reveal the contribution of both shallow and deep traps upon deposition of urea units onto the NPs. It could be concluded that the deposition of polyurea on NPs results in a bi-modal distribution of trap depths that are related to each monomer in the urea units and can lead to a reduction of space charge formation at filler-polymer interfaces. MLD offers a promising tool for tailoring the interfacial interactions in dielectric NCs.