We recently reported (R. Castro Contreras, B. Guicheret, B. F. Machado, C. Rivera-Cárcamo, M. A. Curiel Alvarez, B. Valdez Salas, M. Ruttert, T. Placke, A. Favre Réguillon, L. Vanoye, C. de Bellefon, R. Philippe and P. Serp, J. Catal., 2019, 372, 226–244) that a structure/activity correlation exists in Pd/C catalysts for myrcene hydrogenation, which integrates the Pd dispersion, and the surface concentration of oxygen groups and defects of the support. Here, through a combined experimental–theoretical study, we provide an explanation of the influence of these three structural characteristics of Pd/C catalysts for alkene hydrogenation. Highly dispersed Pd nanoparticles (PdNP) are necessary to activate dihydrogen. A high concentration of surface defects on the support is necessary to stabilize Pd single atoms (PdSA), which coexist with PdNP on Pd/C catalysts. A high concentration of oxygenated surface groups is also necessary on the support to allow hydrogen spillover. We demonstrate that such a combination allows cooperative catalysis to operate between PdNP and PdSA that involves the formation of PdSA–H species, which are much more active than PdNP–H for alkene hydrogenation but also isomerization. Importantly, we also report an efficient method to control the ratio between PdSA and PdNP in Pd/C catalysts of similar loadings and show that the control of this ratio allows the development of a new generation of stable and highly active catalysts integrating the ultra-rational use of precious metals in short supply. Indeed, for myrcene hydrogenation, activity variations of several orders of magnitude were measured as a function of the value of this ratio.