2,2′-Bipyridine (bipy) and an imidazolium-functionalized bipy ligand were used in the synthesis of palladium nanoparticles in water and in ionic liquid. The function of such ligands was twofold: first, as stabilizing agents to prevent the agglomeration of the nanoparticles during synthesis, and second, to act as permanent catalyst modifiers. The N-modified Pd nanoparticles were subsequently deposited onto Carbon Nanofiber-based structured supports and tested in the liquid-phase hydrogenation of 1-hexyne. The catalysts were found to be significantly more selective (up to 98.5% at 25% conversion) than a reference catalyst with non-modified Pd nanoparticles on the same support (88%). Moreover, the high selectivity was maintained up to full conversion, and thus, the over-hydrogenation was suppressed due to a site-blocking effect of the N-containing ligands. The imidazolium-functionalized bipy ligand was found to interact more strongly with the nanocarbon support reinforcing Pd anchoring and reducing leaching into the liquid media.