Magnetic cobalt nanoparticles coated with a thin carbon shell were produced by means of a scalable method based on hydrogen reduction synthesis. The presence of oxidized groups on the surface of the carbon shell enabled the reaction with alkoxysilanes bearing amino and thiol reactive functions under mild conditions, and therefore the formation of a thin functional silane layer which holds the potential for further modification in consideration of specific applications, e.g., in the separation and catalysis fields. The magnetic nanoparticles bearing surface thiol groups were also used in metal adsorption tests. These nanoparticles could efficiently adsorb not only gold from a chloride salt aqueous solution, but also several other metals when incubated in a thiocyanate-leached solution obtained from crushed printed circuit boards. The combination of a scalable production method with a simple and versatile surface modification strategy opens up a wide array of potential industrial applications in the fields of separation, sensing, and biomedical devices.