Palladium nanoparticles were firstly stabilized with metal–organic framework-derived porous carbon for biofuel upgrade, where the catalyst wettability is crucial. The remarkable catalytic performance of Pd/NPC-ZIF-8 in water can be attributed to the well-dispersed and electron-rich Pd sites, high surface area and hierarchical pores, as well as the favorable hydrophilicity of NPC-ZIF-8.