Partial hydrogenation of soybean oil (SO)-derived biodiesel, as fatty acid methyl esters (FAMEs), over mesoporous palladium (Pd)/SBA-15 materials was examined in a semi-batch reactor. The amount of Pd/SBA-15 catalyst was varied from 0.5-1% by weight (wt%) of the SO feedstock. The selectivity of saturated FAMEs (C18:0), which contribute to an excellent oxidative stability but undesirable cold flow properties, over the Pd/SBA-15 catalyst at different wt% was poor after a 4-h reaction period. To improve the catalytic performance, zirconium (Zr) species were incorporated in the SBA-15, resulting in Zr-SBA-15 with tunable acidity and pore properties. Partial hydrogenation of SO-FAME over 0.75 wt% Pd/xZr-SBA-15 catalysts (where x is the Zr/silicon (Si) molar ratio and ranged from 0.01 to 0.11) was performed for 2 h. The catalytic performance and the selectivity towards trans-monounsaturated FAMEs (trans-C18:1), in terms of the turnover frequency (TOF) and trans-C18:1/cis-C18:1 ratio, respectively, were considered at 10% and 80% conversion levels of diunsaturated FAMEs (C18:2). The incorporation of Zr into SBA-15 resulted in an enhanced TOF due to the greater adsorption of both H-2 and the basic double bonds of FAME molecules on the electron-deficient catalyst surfaces. The TOF for the Pd/xZr-SBA-15 catalysts increased as the Zr/Si molar ratio increased up to 0.07, and then slightly dropped at higher Zr/Si molar ratios, presumably due to the hindrance of adsorbed-reacted FAME molecules with strong adsorption and the worsening of physical properties, i.e. pore width (D-p). The selectivity towards trans-C18:1 was directly correlated with the Zr/Si molar ratio. Since the strong adsorption of FAME molecules took place on the catalyst surface, the high level of trans-C18:1 was consequently generated. The oxidative stability of the partially hydrogenated biodiesels was improved by more than four-fold compared to that of the starting SOFAMEs.