A series of phosphonium-based supported ionic liquid phases (SILPs) was prepared for the immobilization of Rh nanoparticles (Rh@SILP). The influence of systematic variations in the structure of the ionic liquid-type molecular modifiers (anion, P-alkyl chain length) on the formation and catalytic properties of Rh nanoparticles (NPs) was investigated. Both the nature of the anion and the length of the P-alkyl chain were found to have a strong impact on the morphology of the NPs, ranging from small (1.2-1.7 nm) and well-dispersed NPs to the formation of large NPs (9.9-16.5 nm) and/or aggregates. The catalytic properties of the resulting Rh@SILP materials were explored using the hydrogenation of benzylideneacetone and biomass-derived furfuralacetone as model reactions. The changes in ring and C=O hydrogenation activity as a function of the SILP structure and the Rh NPs size allowed for the selective synthesis of products with distinct molecular functionalities.