Site modification and isolation through selective poisoning comprise an effective strategy to enhance the selectivity of palladium catalysts in the partial hydrogenation of triple bonds in acetylenic compounds. The recent emergence of supported hybrid materials matching the stereo- and chemoselectivity of the classical Lindlar catalyst holds promise to revolutionize palladium-catalyzed hydrogenations, and will benefit from an in-depth understanding of these new materials. In this work, we compare the performance of bare, lead-poisoned, and ligand-modified palladium catalysts in the hydrogenation of diverse alkynes. Catalytic tests, conducted in a continuous-flow three-phase reactor, coupled with theoretical calculations and characterization methods, enable elucidation of the structural origins of the observed selectivity patterns. Distinctions in the catalytic performance are correlated with the relative accessibility of the active site to the organic substrate, and with the adsorption configuration and strength, depending on the ensemble size and surface potentials. This explains the role of the ligand in the colloidally prepared catalysts in promoting superior performance in the hydrogenation of terminal and internal alkynes, and short-chain alkynols. In contrast, the greater accessibility of the active surface of the Pd–Pb alloy and the absence of polar groups are shown to be favorable in the conversion of alkynes containing long aliphatic chains and/or ketone groups. These findings provide detailed insights for the advanced design of supported nanostructured catalysts.