Bimetallic clusters can have superior catalytic properties compared to those of monometallic clusters due to synergistic interactions between the constituent metals. Here we show that atom-precise Ag clusters can be used as templates for the design of AgPd bimetallic heterogeneous catalysts using a sequential deposition approach. Atom-precise 2,4-dimethylbenzenethiol-protected Ag25(SR)18 clusters were used as precursors for sequential Pd deposition and the eventual structures of the AgPd bimetallic catalysts were revealed by X-ray absorption spectroscopy (XAS) studies. EXAFS data shows that Ag clusters on carbon supports can be thermally activated at low temperatures and then used as templates for the subsequent sequential reduction of Pd ions to form bimetallic clusters. In AgPd bimetallic catalysts with low Pd loadings, Ag atoms are predominately on the catalyst surface while Pd atoms occupy subsurface sites; however at higher Pd loadings most Pd atoms occupy surface sites. These structural changes play a significant role in the selective hydrogenation of 2-methyl-3-butyn-2-ol (MBY) to 2-methyl-3-buten-2-ol (MBE). Bimetallic AgPd catalysts showed superior activity to monometallic Ag catalysts and higher Ag/Pd ratios led to better MBE selectivity. MBE selectivity of 96.6% was obtained for 12:1-Ag:Pd/carbon catalysts and the selectivity progressively reduced with increased Pd loadings, to 0% for 1:6-Ag:Pd/carbon catalysts, in which only the fully hydrogenated product was formed. This work demonstrates a significant structure–property relationship between the geometry and the catalytic performance of AgPd bimetallic clusters prepared via a sequential deposition strategy.