Heavy metal pollution has become an environmental problem throughout the world because heavy metal can be accumulated into the food chain and bring about serious problems, not only for ecosystems but also for human health. In this study, functional metal-binding proteins (FMBPs) were isolated from a metal-stimulated activated sludge culture with the aim of applying them to an innovative metal removal technology. Activated sludge bacteria was cultured in growth media including copper ion, and the stimulation of protein production by copper ion led to the 14% increase in a quantity of extracted crude proteins per 1 g of bacterial cell pellet (wet). In order to isolate FMBPs, extracted crude proteins were applied to the immobilized metal affinity column in which each of copper, nickel and zinc was used as a ligand. Several FMBPs were succesfully isolated from copper-stimulated bacteria. One of FMBPs (molecular weight of about 40 kDa) exhibited an ability to adsorb all three metals. The multi metal-binding property of this FMBP could be applied to an innovative metal removal technology. Furthermore, isolated FMBPs that could capture only one kind of heavy metal would also be attractive as a metal adsorbent in recovering a specific metal as a resource from wastewater, including several heavy metals.