Noble-metals with carbon-based support remains a typical catalyst in fuel cell applications, but their fabrication is usually complicated and energy intensive. In this work, Shewanella cells are used as an environmentally friendly factory for nano-sized Pd preparation and a precursor for multifunctional carbon support with functionalized surface and heteroatom dopant. With simple KOH activation at 420°C, a highly-porous heteroatom-doped carbon with well-dispersed Pd nanoparticles was derived from the microbial cells. The as-synthesized material exhibited a 2.2-times larger specific mass catalytic activity (at −0.1V vs. Ag/AgCl) towards oxygen reduction reaction, better durability and higher methanol tolerance than commercial Pt/C catalyst. Density functional theory calculations provide a molecular-level insight into the ORR mechanism, and suggest that its great catalytic activity was ascribed to the high reactivity of Pd4 cluster and the N- and O-doped carbon support with vacancy. This work opens a facile, low-cost and eco-friendly approach for hybrid electrocatalyst preparation and provides implications for the expanded application of biogenic nano-sized metal nanoparticles.