Metallothionein-3 (MT3) is one of the four mammalian metallothioneins (MT), and is constitutively synthesized in the brain. MT3 acts both intracellularly and extracellularly in this organ, performing functions related to neuronal growth and physiological metal (Zn and Cu) handling. It appears to be involved in the prevention of neurodegenerative disorders caused by insoluble Cu–peptide aggregates, as it triggers a Zn–Cu swap that may counteract the deleterious presence of copper in neural tissues. The literature data on MT3 coordination come from studies either on apo-MT3 reconstitution or the reaction of Zn–MT3 with Cu2+, an ion that is hardly present inside cells. To ascertain the MT3 metal-binding features in a scenario closer to the reductive cell cytoplasm, a study of the recombinant Zn2+, Cd2+ and Cu+ complexes of MT3, βMT3, and αMT3, as well as the in vitro Zn2+–Cd2+ and Zn2+–Cu+ replacement processes, is presented here. We conclude that MT3 has a Cu–thionein character that is stronger than that of the MT1 and MT2 isoforms – also present in the mammalian brain – which is mainly contributed by its β domain. In contrast, the α domain retains a high capacity to bind Zn2+ ions, and, consequently, the entire MT3 peptide shows a peculiar dual ability to handle both metal ions. The nature of the formed Cu+–MT3 complexes oscillates from heterometallic Cu6Zn4–MT3 to homometallic Cu10–MT3 major species, in a narrow Cu concentration range. Therefore, the entire MT3 peptide shows a high capacity to bind Cu+, provided that this occurs in a nonoxidative milieux. This reflects a peculiar property of this MT isoform, which accurately senses different Cu contents in the environment in which it is synthesized.