The use of supported rhodium nanoparticles (RhNPs) is gaining attention due to the drive for better catalyst performance and sustainability. Silica-based supports are promising for RhNP immobilization because of their thermal and chemical stability. Functionalizing silica allows for the design of catalysts with improved activity for biomass transformations. In this study, we synthesized rhodium nanoparticles (RhNPs) supported on N-functionalized silica-based materials, utilizing SBA-15 as the support and functionalizing it with either nicotinamide or an imidazolium-based ionic liquid. Solid-state 29Si and 13C NMR experiments confirmed successful ligand anchoring onto the silica surface. RhNPs@SBA-15-Imz[NTf2] and RhNPs@SBA-15-NIC were efficiently prepared and extensively characterized, revealing small, spherical, and well-dispersed fcc Rh nanoparticles on the support surface, confirmed by XPS analyses detecting metallic rhodium, Rh(I), and Rh(III) species. The catalytic performance of these materials is assessed in the hydrogenation of biomass-derived substrates, including furfural, levulinic acid, terpenes, vanillin, and eugenol, among others, underscoring their potential in sustainable chemical transformations. The nanocatalysts demonstrated excellent recyclability and resistance to metal leaching over multiple cycles. The study shows that neutral and ionic silica grafting fragments differently stabilize RhNPs, affecting their morphology, size, and interaction with silanol groups, which impacts their catalytic activity.