The authors describe double-shell magnetic nanoparticles functionalized with 2-mercaptobenzothiazole (MBT) to give nanospheres of the type MBT-Fe3O4@SiO2@C). These are shown to be viable and acid-resistant adsorbents for magnetic separation of the heavy metal ions Ni(II), Cu(II) and Pb(II). MBT act as a binding reagent, and the carbon shell and the silica shell protect the magnetic core. Following 12 min incubation, the loaded nanospheres are magnetically separated, the ions are eluted with 2 M nitric acid and then determined by inductively coupled plasma-mass spectroscopy. The limits of detection of this method are 2, 82 and 103 ng LaEuro3/4(1) for Ni(II), Cu(II), and Pb(II) ions, respectively, and the relative standard deviations (for n = 7) are 6, 7.8, and 7.4 %. The protocol is successfully applied to the quantitation of these ions in tap water and food samples (mint, cabbage, potato, peas). Recoveries from spiked water samples ranged from 97 to 100 %.