Developing effective catalysts that can selectively hydrogenate C=C bonds in biodiesel samples is vital as it tackles the major problem of oxidative stability, which greatly limits the utilization of biodiesel as an alternative fuel. In this work, Co, Ni, and Pd catalysts stabilized with the bidentate nitrogen ligands N-(3-(triethoxysilyl)propyl)pyridin-2-ylmethylimine and N-(3-(triethoxysilyl)propyl)picolinamide were synthesized, characterized, and used as pre-catalysts in the transfer hydrogenation of C=C bonds in fatty acid methyl esters. The active catalysts from the Co, Ni, and Pd complexes sequentially hydrogenate the C18:2 chains to C18:1, which is further converted to C18:0 in the FAMEs of both methyl linoleate and jatropha biodiesel. The hydrogenation process was kinetically controlled, and after 3 h it yielded a biodiesel sample that contained 25.83% C16:0, 12.52% C18:2, 41.54% C18:1, 14.47% C18:0 and 3.0% C18:2 isomers. The un-hydrogenated jatropha diesel, hydrogenated jatropha diesel, and a B20 blend of jatropha were tested for susceptibility to oxidation reactions using the Rancimat method and FTIR spectroscopy, and the partial hydrogenation had improved the induction period by 3 h.