We investigated the coating of glass-supported gold nanostructures with polyelectrolyte multilayers. To achieve selective coating of either the metal or the glass, thiol and silane monolayers with different functionalities were used. Self-assembled monolayers of an oligo-(ethylene glycol)-terminated silane on glass allow for complete passivation and fully selective deposition of the polyelectrolytes on the metallic structures. This glass passivation forces more material on the gold than without use of this silane. Gold passivation was achieved on Au(111) but was not successful on the metallic nanostructures, giving rise to polyelectrolytes irregularly deposited on the nanoparticles in the form of blobs.