Deep eutectic solvents (DES) are being increasingly used in electrodeposition because they are considered to be environmentally benign. We report here a single step method for the preparation of Au–Pd core–shell nanoparticles (Au@Pd NPs) on a graphite rod in a DES medium. These ready-to-use mesoporous substrates were prepared by the simultaneous electrodeposition of the in situ formed Au@Pd nanoparticles via an anodic dissolution technique. The fabrication strategy by anodic dissolution in a DES avoided the addition of external stabilizers, reducing agents and metal salt precursors. The core–shell morphology of the nanoparticles was characterized by SEM, while the elemental composition was confirmed by EDAX and cyclic voltammetry. The catalytic characteristics of the Au@Pd nanoparticle modified graphite were systematically studied in the electrochemical oxidation of methanol by cyclic voltammetry, Tafel analysis and activation energy measurements. The Au@Pd NPs exhibited superior catalytic performance over its corresponding monometallic counterparts, viz., AuNPs and PdNPs, prepared under identical conditions. The activation energy requirements of the Au@Pd NP modified graphite electrodes were low, making them potential anode catalysts in alkaline media based methanol fuel cells at ambient temperatures. The method suggested here for the synthesis of mesoporous electrocatalysts is simple, effective and environmentally friendly.