We propose a new method for preparing atom probe tomography specimens from nanoparticles using a fusible bismuth–indium–tin alloy as an embedding medium. Iron nanoparticles synthesized by the sodium borohydride reduction method were chosen as a model system. The as-synthesized iron nanoparticles were embedded within the fusible alloy using focused ion beam milling and ion-milled to needle-shaped atom probe specimens under cryogenic conditions. An atom probe analysis revealed boron atoms in a detected iron nanoparticle, indicating that boron from the sodium borohydride reductant was incorporated into the nanoparticle during its synthesis.