The combination between a sulfonated diphosphine (L) and a cyclodextrin (CD) allowed the preparation of very stable water-soluble ruthenium nanoparticles (RuNPs) that displayed pertinent catalytic performances in hydrogenation of unsaturated substrates with a supramolecular control effect of the cyclodextrin. For comparison purpose, the RuNPs were produced by hydrogenation of the organometallic [Ru(1,5-cyclooctadiene)(1,3,5-cyclooctatriene)] complex under mild conditions (3 bar H2; room temperature) and in the presence of L or a L/CD mixture as stabilizer leading to Ru/L and Ru/L/CD systems, respectively. The so-obtained nanoparticles were fully characterized by complementary techniques. Interestingly, NMR investigations evidenced 1) the strong coordination of the sulfonated diphosphine ligand at the metallic surface and 2) in the presence of cyclodextrin, the formation of an inclusion complex between L and CD that modified the coordination mode of the diphosphine. The investigation of both RuNPs systems in biphasic hydrogenation of unsaturated substrates pointed out relevant differences in terms of reactivity, thus evidencing the influence of the supramolecular interaction at the metallic surface on the catalytic performances of the nanocatalysts. This work took advantage of the supramolecular properties of a cyclodextrin to modulate the surface reactivity of diphosphine-stabilized ruthenium nanoparticles and may open new opportunities in the field of nanocatalysis.