Alkanethiolate-capped palladium nanoparticles (PdNPs) have previously been synthesized using a modified Brust-Schiffrin synthesis (using alkyl thiosulfate instead of alkanethiol), in which the nanoparticle core size is established during alkyl thiosulfate ligand passivation of the nanoparticle nucleation-growth initiated by borohydride reduction. Due to the dependence of core size on amount of ligand present, surface ligand density decreases with increasing core size. Herein we present a method in which core size is established independent to ligand addition, allowing the formation of PdNPs with similar core sizes, yet different surface ligand density. In this method, core size is established during the temporary passivation of growing nanoparticles by borohydride and tetra-N-octylammonium bromide (TOAB), allowing nucleation to reach completion. Various molar equivalents of alkyl thiosulfate are then added, prompting the replacement of borohydride and TOAB and the formation of alkanethiolate-capped PdNPs. The resulting PdNPs were characterized via 1H NMR, transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and inductively coupled plasma atomic emission spectroscopy (ICP-AES). Overall enhanced catalytic activity of hydrogenation/isomerization of dienes and alkenes was observed for PdNPs with a lower ligand density, proving the isolated effect of surface ligand density from other variations such as core size and shape. Surface ligand density is also shown to have an effect on hydrogenation/isomerization product selectivity for certain model catalytic reactions. Binary ligand PdNPs were also synthesized via the reversed thiosulfate addition method and surface morphology was characterized via nuclear Overhauser effect spectroscopy (NOESY). The influence of surface morphology on catalytic activity and selectivity are also probed.