The microstructural design of ceramics is relevant to tune their properties. Nanostructuring can drastically modify ceramic properties because of enhanced interfacial effects, although the creation of such structures in ceramics is still challenging because of the interfacial reaction and grain growth at elevated temperatures during sintering. Here, we demonstrate densification of core–shell nanoparticles consisting of Fe3O4 (core particle, 20 nm diameter) and SiO2 (shell layer, 2 nm thick) with over 90% of theoretical density below 500°C, which was achieved by facilitating plastic flow of amorphous SiO2 under high pressure below its glass transition temperature. Thus, grain growth of the core nanoparticles was strongly suppressed, and the core nanoparticles remained separated by an amorphous layer in the final microstructure reflecting the original core–shell nanostructure. We also analyzed the densification behavior on the basis of a power law creep model, and estimated the pressures required to attain full density.