Silicon dioxide thin films are widely used as dielectric layers in microelectronics and can also be engineered on silicon wafers. It seems counterintuitive that electrochemical reactions could occur on such an insulator without relying on tunnelling current. Here we report electrochemistry based on electron transfer through a thin insulating layer of thermally grown silicon dioxide on highly n-doped silicon. Under a negative electrical bias, protons in the silicon dioxide layer were reduced to hydrogen atoms, which served as electron mediators for electrochemical reduction. Palladium nanoparticles were preferentially formed on the dielectric layer and enabled another hydrogen-atom-mediated electrochemistry, as their surfaces retained many electrogenerated hydrogen atoms to act as a 'hydrogen-atom reservoir' for subsequent electrochemical reduction. By harnessing the precisely controlled electrochemical generation of hydrogen atoms, palladium-copper nanocrystals were synthesized without any surfactant or stabilizer on the silicon dioxide layer.