The development of practical multivalent-ion batteries critically depends on the identification of suitable positive electrode materials. To gain a better understanding of the intercalation chemistry of multivalent ions, model frameworks can be used to study the distinct specificities of possible multivalent ions, thus expanding our knowledge on the emerging “beyond Li battery” technology. Here, we compare the intercalation chemistry of Mg2+, Zn2+, and Ca2+ ions in a disordered layered-type structure featuring water interlayers and cationic vacancies as possible host sites. The thermodynamics of cation-inserted reactions performed on the model structure indicated that these reactions are thermodynamically favorable with Zn2+ being the least stable ion. Galvanostatic measurements confirmed that the structure is inactive toward Zn2+ intercalation, while Mg2+ can be reversibly inserted (0.37 Mg2+ per formula unit) with minor changes in the atomic arrangement, as demonstrated by pair distribution function analysis. Moreover, we demonstrate that nonsolvated Mg2+ was intercalated in the structure. Finally, the intercalation of Ca2+ performed at 100 °C with Ca(BF4)2 in propylene carbonate induced the collapse of the layered structure releasing water molecules that contribute to the degradation of the electrolyte, as revealed by the presence of CaF2 at the electrode level. The decomposition of the structure led to the formation of an electrochemically active phase featuring a strong long-range disorder, yet a short-range order close to that found in perovskite structures, particularly with corner-shared TiO6 octahedra. We, hence, hypothesize that defective CaTiO3-based perovskite could be explored as viable cathode materials for rechargeable Ca-based batteries.