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Biodiesel obtained through the transesterification in methanol of vegetable oils, such as soybean oil (SO) and waste cooking oil (WCO), cannot be used as a biofuel for automotive applications due to the presence of polyunsaturated fatty esters, which have a detrimental effect on oxidation stability (OS). A method of upgrading this material is the catalytic partial hydrogenation of the fatty acid methyl ester (FAME) mixture. The target molecule of the partial hydrogenation reaction is monounsaturated methyl oleate (C18:1), which represents a good compromise between OS and the cold filter plugging point (CFPP) value, which becomes too high if the biodiesel consists of unsaturated fatty esters only. In the present work, polymer-supported palladium (<i>Pd-pol</i>) and nickel (<i>Ni-pol</i>) nanoparticles were separately tested as catalysts for upgrading SO and WCO biodiesels under mild conditions (room temperature for <i>Pd-pol</i> and T = 100 °C for <i>Ni-pol</i>) using dihydrogen (<i>p</i> = 10 bar) as the reductant. Both catalysts were obtained through co-polymerization of the metal containing monomer M(AAEMA)₂ (M = Pd, Ni; AEEMA⁻ = deprotonated form of 2-(acetoacetoxy)ethyl methacrylate)) with co-monomers (ethyl methacrylate for Pd and <i>N,N</i>-dimethylacrilamide for Ni) and cross-linkers (ethylene glycol dimethacrylate for Pd and <i>N,N’</i>-methylene bis-acrylamide for Ni), followed by reduction. The <i>Pd-pol</i> system became very active in the hydrogenation of C=C double bonds, but poorly selective towards the desirable C18:1 product. The <i>Ni-pol</i> catalyst was less active than <i>Pd-pol</i>, but very selective towards the mono-unsaturated product. Recyclability tests demonstrated that the Ni-based system retained its activity and selectivity with both the SO and WCO substrates for at least five subsequent runs, thus representing an opportunity for waste biomass valorization.