A key aspect of nanoscience is to control the assembly of complex materials from a "bottom-up" approach. The self-assembly and self-organization of small ligands at the surface of nanoparticles represent a possible starting route for the preparation of (bio)nanomaterials with precise (bio)physical and (bio)chemical properties. However, surface characterization and elucidation of the structure-properties relationship, essential to envisioning such control, remain challenging and are often poorly investigated. This Topical Review aims to discuss different levels of surface characterization, giving an overview of the experimental and computational approaches that are used to provide insights into the self-assembled monolayer with molecular details. The methods and strategies discussed focus on the characterization of self-assembled monolayers at the gold nanoparticle surface, but most of them could also be applied to other types of nanoparticles.