AbstractCatalytic reduction of organic pollutants using metal nanoparticles (MNPs) as nanocatalyst is a promising approach. The widespread application of MNPs have led to an increase demand for their production. The green biosynthesis of MNPs using microbes is becoming increasingly important as they are benign and environmentally friendly. In this work, Deinococcus wulumuqiensis (D. wulumuqiensis) with high resistance to stresses was applied for the green preparation of different MNPs, including palladium nanoparticles (Pd NPs), silver nanoparticles (Ag NPs), and Pd−Ag bimetallic nanoparticles (Pd−Ag BNPs). The resultant MNPs exhibited a face‐centered cubic structure, with average size of 6.70 (Pd NPs), 6.24 (Ag NPs), and 6.13 nm (Pd−Ag BNPs), respectively. FT‐IR spectra indicated that the proteins and polysaccharides expressed by D. wulumuqiensis could potentially contributed to the formation of MNPs. The application of as‐prepared biocatalyst in catalytic degradation of pollutant dyes demonstrated that Pd−Ag BNPs had greater degradation ability of 4‐nitrophenol (95.1 %) and Rhodamine B (85.1 %) than monometallic nanoparticles. The pseudo‐first‐order kinetics results further indicated the superior catalytic ability of Pd−Ag BNPs, with rate constant of 0.450±0.009 (4‐nitrophenol) and 1.54×10−2 min−1 (Rhodamine B), respectively. Thus, the present study confirms that D. wulumuqiensis represents a promising candidate for the biosynthesis of Pd‐based nanoparticles with small size, which exhibited potential applications as bionanocatalyst in the degradation of water pollutants.