Uniform Pd nanocrystals of cubic, octahedral and cube-octahedral shapes were synthesized via a solution-phase method using two stabilizers: poly (vinyl pyrrolidone) (PVP) and di-2-ethylhexylsulfoccinate (AOT) and tested in the hydrogenation of 2-methyl-3-butyn-2-ol. The AOT-stabilized Pd nanocrystals were found to be an order of magnitude more active, but less selective than those stabilized by PVP. This could be attributed to a stronger interaction of PVP with surface Pd by adsorbed N-containing groups. The results obtained were rationalized applying a two-site Langmuir–Hinshelwood kinetic model that allowed predicting 3–4 nm cubic or octahedral nanocrystals stabilized by AOT as the optimum active phase ensuring the highest production rate of target MBE.