Control of heterogeneous catalytic sites through their surrounding chemical environment at an atomic level is crucial to catalyst design. We synthesize Pd nanoclusters (NCs) in an atomically tunable chemical environment using isoreticular metal–organic framework (MOF) supports (Pd@UiO-66-X, X = H, NH2, OMe). In an aerobic reaction between benzaldehyde and ethylene glycol, these catalysts show product distributions that are completely altered from the acetal to the ester when we change the functional groups on the MOF linkers from −NH2 to −H/–OMe. Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) studies, along with density functional theory (DFT) calculations, show that the coordination of the −NH2 groups to the Pd NCs could weaken their oxidation capability to a greater extent in comparison to that of the −OMe group. Moreover, the limited number of −NH2 groups per cavity in the MOF change the electronic properties of the Pd NCs while still leaving open sites for catalysis.