We describe a facile strategy to synthesize hybrid nanocapsules with an oil core for hindering interactions between payloads and silica shell. Polycaprolactone/silica nanocapsules are synthesized by an interfacial sol-gel process occurring simultaneously with internal phase separation of the polymer produced by a miniemulsion-solvent evaporation technique. The localization of the polycaprolactone in the nanocapsules is depending on the ratio between polymer and silica. Formation of hybrid nanocapsules is found to significantly hinder interactions of drugs such as ibuprofen and carbamazepine with the silica surface.