Updated project metadata. Many studies have been conducted on microbial reduction of Pd (II) to palladium nanoparticles (PdNPs) due to the environmental friendliness, low cost and the decreased toxicity of Pd (II) ions. In this study, we investigate the reduction mechanism of Pd (II) by Bacillus megaterium Y-4 through proteomics. Our results revealed that B. megaterium Y-4 may use the endogenous electron donor (NAD(P)H) generated by nirB, tdh and fabG and reductase to reduce Pd (II) to PdNPs. The expression levels of fabG, tdh, gudB and rocG that generates NAD(P)H were further increased, and the amount of reduced PdNPs was further increased in the presence of exogenous electron donor sodium formate. Endogenous electron mediators such as quinones and flavins in B. megaterium Y-4, can further enhance Pd (II) reduction. The findings provided invaluable information regarding the reduction mechanism of Pd (II) by B. megaterium Y-4 at the proteome level.