Suppressing aromatic ring reduction in noble-metal-catalyzed H/D exchange reactions remains a challenge. This drawback may be overcome by finding a synergetic effect in bimetallic nanoparticles (NPs). Herein, we report the synthesis of bimetallic lipo- and water-soluble Ru/Ir NPs. They were characterized by state-of-the-art techniques such as transmission electron microscopy (TEM), high-resolution TEM, attenuated total reflection Fourier transform infrared, powder X-ray diffraction, and solid-state nuclear magnetic resonance. These NPs were found to disperse in both organic and aqueous media because of the stabilization and coordination of adequate N-heterocyclic carbene (NHC) ligands to the NP surface. They were tested in the deuteration of 2-phenylpyridine, 2-methyl-naphthylamine, 5,6,7,8-tetrahydro-naphthtylamine, and l-lysine using D2 as the isotopic source. Bimetallic NPs showed an unusual selectivity toward the H/D exchange of 2-phenylpyridine, deuterating not only the expected C–H positions close to the N atom but also remote positions on the heterocycle. Additionally, reduction of the aromatic rings, which is a common undesired side reaction catalyzed by Ru NPs, was not observed. These outcomes, rationalized by a synergetic effect of both metals, are enhanced when NHC ligands are on the surface in comparison to model catalysts stabilized by polyvinylpyrrolidone. With regard to non-aromatic substrates, CH2-α and CH2-ε positions with respect to the amino acid group of l-lysine were fully deuterated, while moderate deuteration of the γ position was observed as the iridium content was increased in the bimetallic system.