Selective hydrogenation of phenol is a sustainable alternative to cyclohexane oxidation for the production of cyclohexanone. However, over-hydrogenation of cyclohexanone to cyclohexanol is thermodynamically favorable, limiting its selectivity. Here, we report an unprecedented cyclohexanone selectivity (>99.9%) in continuous-flow phenol hydrogenation using an electron-deficient Pd catalyst. The Pd atom exists in a unique Pd–N5C4 structure in which it is coordinated with four quasi-planar N atoms and one axial N atom in the first shell and an additional four C atoms in the second shell that lie on the curved surface of a pore in ordered mesoporous carbon. The Pd site has a d charge depletion of 1.18 e that prevents cyclohexanone adsorption, which is therefore exclusively produced. Bonding the Pd atom to a curved plane of carbon atoms is an effective way to control the d charge of Pd and increase its selectivity for the green synthesis of fine chemicals.