General interest in solvent-free catalytic processes is driven by the development of environmentally and economically acceptable procedures. Such processes require the use of highly active and stable catalysts. This study reports on the synthesis, characterization, and kinetic evaluation of two highly active Pd catalysts supported on different carbons support, i.e., multi-walled carbon nanotubes (CNT) and few-layer graphene (FLG). These catalysts, with similar Pd loading (∼2 wt%) and containing both Pd single atoms (PdSA) and nanoparticles (PdNP), were systematically tested for solvent-free total hydrogenation of squalene (SQE) to obtain high-purity squalane (SQA). Thanks to the unique cooperative catalysis between PdSA and PdNP involving H-spillover, the activities of both catalysts were high compared to catalysts described in the literature. Solvent-free total hydrogenation of SQE could be performed under mild conditions (120 °C, 20 bar H2, 4 h) using ultralow Pd loading (60 ppm). However, since this reduction reaction is highly exothermic (ΔHR= − 765 kJ.mol−1), heat management during the reactor operation with these highly active catalysts is crucial to avoid deactivation and thermal runaway. Under these conditions, Pd/FLG was highly active but deactivated, unlike Pd/CNT, which still has high activity, but does not deactivate. Characterizations (ICP, XPS, Raman, TPD-MS, HAADF-STEM) of the Pd/FLG catalyst before and after reaction, supported by calculations based on density functional theory, allowed us to propose a new mechanism of catalyst deactivation involving the chemical reduction of specific surface oxygen groups of the carbon support induced by H-spillover.