Hydrophilic silica particles need to be hydrophobized to be encapsulated in a polymeric environment, which can be achieved by different methods. We report on the relationship between different hydrophobization techniques of silica and the final structure of poly(methyl methacrylate)/silica hybrid nanoparticles obtained by miniemulsion polymerization. Hydrophobization by cetyltrimethylammonium chloride (CTMA-Cl) uses the ionic interaction between the positively charged ammonium salt and the negatively charged silica surface, as shown by isothermal titration calorimetry. In this case, the interaction between polymer and silica surface needs to be enhanced, so 4-vinylpyridine (4-VP) was used as a co-monomer. Alternatively, the condensation reactions of 3-methacryloxypropyltrimethoxysilane (MPS) and octadecyltrimethoxysilane (ODTMS) were used to provide a covalent bond to the silica surface. The condensation reaction of the trimethoxysilane groups onto the silica surface was proven by Fourier transform infrared spectroscopy and thermogravimetric analysis. Hybrid nanoparticles were successfully formed with silica particles functionalized with the different functionalization agents. However, the structure of the resulting hybrid particles (i.e., the distribution of the silica particles within the polymer matrix) depends on the agent. The MPS-functionalized silica particles copolymerize with poly(methyl methacrylate), leading to a fixation of the silica particles inside the polymer and to a homogeneous distribution. The CTMA-Cl-and ODTMSfunctionalized silica particles cannot copolymerize, but aggregate at the interface, leading to a Janus-like structure.