Intermetallic compounds are garnering increasing attention as efficient catalysts for improved selectivity in chemical processes. Here, using a ship-in-a-bottle strategy, we synthesize single-phase platinum-based intermetallic nanoparticles (NPs) protected by a mesoporous silica (mSiO2) shell by heterogeneous reduction and nucleation of Sn, Pb, or Zn in mSiO2-encapsulated Pt NPs. For selective hydrogenation of furfural to furfuryl alcohol, a dramatic increase in activity and selectivity is observed when intermetallic NPs catalysts are used in comparison to Pt@mSiO2. Among the intermetallic NPs, PtSn@mSiO2 exhibits the best performance, requiring only one-tenth of the quantity of Pt used in Pt@mSiO2 for similar activity and near 100% selectivity to furfuryl alcohol. A high-temperature oxidation-reduction treatment easily reverses any carbon deposition-induced catalyst deactivation. X-ray photoelectron spectroscopy shows the importance of surface composition to the activity, while density functional theory calculations reveals that the enhanced selectivity on PtSn compared to Pt is due to the different furfural adsorption configurations on the two surfaces.