We have examined the uptake mechanisms of platinum-group-metals (PGMs) and molybdenum (Mo) ions into Prussian blue nanoparticles (PBNPs) in a nitric acid solution for 24-h sorption test, using inductively coupled plasma atomic emission spectroscopy, powder XRD, and UV–Vis-NIR spectroscopy in combination with first-principles calculations, and revealed that the Ru4+ and Pd2+ ions are incorporated into PBNPs by substitution with Fe3+ and Fe2+ ions of the PB framework, respectively, whereas the Rh3+ ion is incorporated into PBNPs by substitution mainly with Fe3+ and minorly with Fe2+ ion, and Mo6+ ion is incorporated into PBNPs by substitution with both Fe2+ and Fe3+ ions, with maintaining the crystal structure before and after the sorption test. Assuming that the amount of Fe elusion is equal to that of PGMs/Mo substitution, the substitution efficiency is estimated to be 39.0% for Ru, 47.8% for Rh, 87% for Pd, and 17.1% for Mo6+. This implies that 0.13 g of Ru, 0.16 g of Rh, 0.30 g of Pd, and 0.107 g of Mo can be recovered by using 1 g PBNPs with a chemical form of KFe(III)[Fe(II)(CN)6].