We report a comprehensive study of the interaction of transition and heavy metal ions with graphene quantum dots-capped silver nanoparticles (AgGQDs) using different spectroscopic and microscopic techniques. High-resolution transmission electron microscopy studies show that the interaction of metal ions with AgGQDs leads to the formation of metal oxides, the formation of zerovalent metals, and the aggregation of Ag nanoparticles (AgNPs). The metal ions may interact with AgGQDs through selective coordination with -OH and -COOH functionalities, adsorption on the graphene moiety, and directly to AgNPs. For instance, the interaction of Cd2+ with AgGQDs altered the spherical shape of AgNPs into a chain-like structure. On the contrary, the formation of PbO is observed after the addition of Pb2+ to AgGQDs. Interestingly, the interaction of AgGQDs with Hg2+ results in the complete dissolution of Ag0 from the surface of GQDs and subsequent deposition of Hg0 on the graphene moiety of GQDs. Unlike transition metal ions, Cd2+, Pb2+, and Hg2+ can adsorb strongly on the graphene surface at the bridge, hollow, and top sites, respectively. This special interaction of heavy metal ions with the graphene surface would decide the mechanistic pathway in which the reaction proceeds. The transition metal ions Cu2+, Zn2+, Co3+, Mn2+, Ni2+, and Fe3+ induced the aggregation of AgNPs.