The industrial implementation of hydrogen peroxide as a green oxidant requires the development of efficient catalytic systems for its direct synthesis from molecular oxygen and hydrogen. Bimetallic Au–Pd nanoparticles supported on acid pre-treated ordered CMK-3 carbon catalysts show high H2O2 productivities and high H2 selectivities (>99%). Encapsulation of the nanoparticles within the pore network lead to stable small size (∼2 nm) particles. This paper reveals that the acid pre-treatment, does not only improve the metal dispersion of metals but most importantly, it promotes their gold enrichment, dramatically decreasing the parallel H2O2 decomposition, which is key for the economic feasibility of the process.