The functionalization of the surface of nanomaterials is a key approach to improve their stability, tune their reactivity and confer them specific properties. However, the mapping of functional groups at the nanometer scale remains difficult to achieve. This concerns not only the chemical nature of these groups, but also their spatial distribution. It is particularly challenging when it comes to organic groups and non-planar objects such as nanoparticles and necessitates the development of strategies beyond the techniques (i.e. chemical analysis and imaging). Here we report such a strategy for mapping amine groups on the surface of silica particles using chemicallymodified gold colloids, which are used as tags to specifically and spatially identify these organic groups under electron microscopy. A complete understanding of the correlation between the spatial distribution of gold colloids and the chemical state of the silica particle surface, as obtained by Xray photoelectron spectroscopy, is presented. The range of suitability and reliability of this strategy for mapping organic groups at nanomaterial interfaces is assessed, and its implications for biofunctional nano-objects where interdistance and clustering of signaling biomolecules are of paramount importance are discussed.