Abstract Palladium on carbon (Pd/C) is the most widely available heterogeneous hydrogenation catalyst both in academia and industry, however catalyst selectivity is poor and product purification and catalyst recycling can be difficult. Here we explored magnetite (Fe3O4) as a catalyst support for palladium because of its interesting magnetic properties. Magnetite nanoparticles were chemically modified with N- and S-donor groups by alkoxyorganosilane grafting and they were used as support for the preparation of magnetically recoverable Pd catalysts. We investigated the influence of different functional groups grafted on the surfaces of magnetite on the catalytic properties of palladium with special attention on the hydrogenation of alkyne and alkene groups. The discrimination between carbon–carbon triple and double bonds is a very important feature of those catalysts and was also observed in competitive experiments containing alkyne–alkene mixtures. No hydrogenation of olefinic bonds was observed as far as an acetylenic compound is present. Even though the hydrogenation of pure olefins occurs with reaction rates comparable with Pd/C, the commercial catalyst deactivates upon recycle and our catalyst is active for several successive reactions.