Commercial carbon nanofibers with different graphitic structure and commercial multiwall carbon nanotubes (CNT) were chemically modified in order to introduce specific alkyl ligands on their surface. Palladium catalysts have been prepared using these modified supports and subsequently tested in the partial hydrogenation of 1,3-butadiene under conditions of excess hydrogen. Herein, we used thermogravimetry (TG), temperature programmed desorption (TPD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and nitrogen adsorption at 77 K techniques in order to characterize both supports and catalysts. We focus on testing the effects of support surface functionalities either on morphology of supported palladium (Pd) nanoparticles (NPs) or on their catalytic performances. High selectivity to butenes was obtained with the catalysts prepared over supports containing alkyl chains, while over-hydrogenation to butane took place over oxygen-containing functional groups. Nicely the catalysts with modified supports minimize the secondary hydrogenation of butenes even at high conversions. Therefore, Pd NPs on modified nano-carbon catalysts may open up more opportunities to optimize the activity and the selectivity for partial hydrogenation reactions.