The combination of complementary characterization techniques such as SEM (Scanning Electron Microscopy), T-SEM (Scanning Electron Microscopy in Transmission Mode), EDX (Energy Dispersive X-ray Spectroscopy) and SAM (Scanning Auger Microscopy) has been proven to be a powerful and relatively quick characterization strategy for comprehensive morphological and chemical characterization of individual silica and titania nanoparticles. The selected “real life” test materials, silica and titania, are listed in the OECD guidance manual as representative examples because they are often used as commercial nanomaterials. Imaging by high resolution SEM and in the transmission mode by T-SEM allows almost simultaneous surface and in-depth inspection of the same particle using the same instrument. EDX and SAM enable the chemical characterization of bulk and surface of individual nanoparticles. The core–shell properties of silica based materials are addressed as well. Titania nominally coated by silane purchased from an industrial source has been found to be inhomogeneous in terms of chemical composition.