In this work, we present a comprehensive comparison of time-of-flight secondary ion mass spectrometry (TOF-SIMS) and scanning transmission electron microscopy combined with energy-dispersive X-ray spectroscopy (STEM/EDX), which are currently the most powerful elemental characterization techniques in the nano- and microscale. The potential and limitations of these methods are verified using a novel dedicated model sample consisting of Al nanoparticles buried under a 50 nm thick Cu thin film. The sample design based on the low concentration of nanoparticles allowed us to demonstrate the capability of TOF-SIMS to spatially resolve individual tens of nanometer large nanoparticles under ultrahigh vacuum (UHV) as well as high vacuum (HV) conditions. This is a remarkable achievement especially taking into account the very small quantities of the investigated Al content. Moreover, the imposed restriction on the Al nanoparticle location, i.e., only on the sample substrate, enabled us to prove that the measured Al signal represents the real distribution of Al nanoparticles and does not originate from the artifacts induced by the surface topology. The provided comparison of TOF-SIMS and STEM/EDX characteristics delivers guidelines for choosing the most optimal method for efficient characterization of nano-objects.