The need for sustainable and large-scale energy supply has led to significant development of renewable energy and energy storage technologies. Divalent metal ion (Mg, Ca, and Zn) batteries are promising energy storage technologies for the sustainable energy future, but the need for suitable electrode materials have limited their commercial development. This paper investigates, at the atomic scale, the adsorption and migration of Mg, Ca, and Zn on pristine and defective graphene surfaces, to bring insight into the metal storage and mobility in graphene and carbon-based anodes for divalent metal ion batteries. Such atomistic studies can help address the challenges facing the development of novel divalent metal battery technologies, and to understand the storage differences between divalent and monovalent metal-ion batteries. The adsorption of Ca on the graphene-based system is shown to be more energetically favorable than the adsorption of both Mg and Zn, with Ca showing adsorption behavior similar to the monovalent ions (Li, Na, and K). This was further investigated in terms of metal migration on the graphene surface, with much higher migration energy barriers for Ca than for Mg and Zn on the graphene systems, leading to the trapping of Ca at defect sites to a larger extent.