Structures of nanoparticles are becoming increasingly complex as they keep acquiring multi-functionality. These nanoparticles often adopt a core–shell structure and comprise different types of materials. Their outer shell forms the interface between the particle core and the environment. and its porosity governs any material exchange. Current techniques for measuring porosity exist for microscopic samples but techniques adapted to nanoscale samples are wanting. We probed indirectly the porosity of an outer silica shell grown over silica nanospheres by means of metal-chelating agents located in the interior of the nanospheres. Using a high-tilt cryo-holder, we performed electron tomography with a high-angle annular dark field detector to determine the 3D structure of these multi-shell nanocomposites. Contamination was significantly reduced at 104 K. Tomographic reconstructions revealed the distribution of functional domains binding metal ions that had penetrated the porous silica shell around the core particle.