The structural characterization of supported molecular catalysts is challenging due to the low concentration of surface sites and the presence of several organic/organometallic surface groups resulting from the often complex surface chemistry associated with support functionalization. Here, we provide a complete atomic-scale description of all surface sites in a silica-supported iridium-N-heterocyclic carbene (Ir-NHC) catalytic material, at all stages of its synthesis. By combining a suitable isotope labelling strategy with the implementation of multi-nuclear dipolar recoupling DNP enhanced NMR experiments, the 3D structure of the Ir-NHC sites, as well as that of the synthesis intermediates were determined. As a significant fraction of parent surface fragments does not react during the multi-step synthesis, site-selective experiments were implemented to specifically probe proximities between the organometallic groups and the solid support. The NMR-derived structure of the iridium sites points to a well-defined conformation. By interpreting extended x-ray absorption fine structure (EXAFS) spectroscopy and chemical analysis data augmented by computational studies, the presence of two coordination geometries is demonstrated: Ir-NHC fragments coordinated by a 1,5-cyclooctadiene and one Cl ligand, as well as, more surprisingly, a fragment coordinated by two NHC and two Cl ligands. This study demonstrates a unique methodology to disclose individual surface structures in complex, multi-site environments, a long-standing challenge in the field of heterogeneous/supported catalysts, while revealing new, unexpected structural features of metallo-NHC supported substrates. It also highlights the potentially large diversity of surface sites present in functional materials prepared by surface chemistry, an essential knowledge to design materials with improved performances.