Characterization of core-shell type nanoparticles in 3D by transmission electron microscopy (TEM) can be very challenging. Especially when both heavy and light elements coexist within the same nanostructure, artifacts in the 3D reconstruction are often present. A representative example would be a particle comprising an anisotropic metallic (Au) nanoparticle coated with a (mesoporous) silica shell. To obtain a reliable 3D characterization of such an object, a dose-efficient strategy is proposed to simultaneously acquire high-angle annular dark-field scanning TEM and annular dark-field tilt series for tomography. The 3D reconstruction is further improved by applying an advanced masking and interpolation approach to the acquired data. This new methodology enables us to obtain high-quality reconstructions from which also quantitative information can be extracted. This approach is broadly applicable to investigate hybrid core-shell materials.