Intermetallic compounds offer unique opportunities for atom-by-atom manipulation of catalytic ensembles through precise stoichiometric control. The (Pd, M, Zn) γ-brass phase enables the controlled synthesis of Pd-M-Pd catalytic sites (M = Zn, Pd, Cu, Ag and Au) isolated in an inert Zn matrix. These multi-atom heteronuclear active sites are catalytically distinct from Pd single atoms and fully coordinated Pd. Here we quantify the unexpectedly large effect that active-site composition (that is, identity of the M atom in Pd-M-Pd sites) has on ethylene selectivity during acetylene semihydrogenation. Subtle stoichiometric control demonstrates that Pd-Pd-Pd sites are active for ethylene hydrogenation, whereas Pd-Zn-Pd sites show no measurable ethylene-to-ethane conversion. Agreement between experimental and density-functional-theory-predicted activities and selectivities demonstrates precise control of Pd-M-Pd active-site composition. This work demonstrates that the diversity and well-defined structure of intermetallics can be used to design active sites assembled with atomic-level precision.