The formation of host–guest cyclic architectures, built up through the self-condensation process of [Mo2O2S2]2+ oxothiocations around linear dicarboxylate ions such as adipate (Adip2−), suberate (Sub2−) and azelaate (Azel2−) anions is reported. The complexes [Mo12Adip]2−, [Mo12Sub]2− and [Mo14Azel]2− have been characterized in the solid state by X-ray diffraction and in solution by 1H NMR in different solvents (D2O, DMF, DMSO and CD3CN). The host–guest dynamics appear to be dependent on the nature of the system and are mainly governed by mutual adaptability between the host and the guest. 1H NMR DOSY experiments show systematic differences, either positive or negative between the experimental and calculated molecular weights which appear to be correlated with the charge of the anion. The relative stabilities of the twelve-membered rings containing the Adip2−, Pim2− (pimelate) or Sub2− anions were determined experimentally and decrease according to the order [Mo12Adip]2− > [Mo12Pim]2− > [Mo12Sub]2−. The host–guest adaptability depends on the length of the carbon chain and gives rise to selective encapsulation processes. Finally, theoretical DFT investigations in the gas phase yielded conformations whose symmetry and geometrical parameters proved consistent with X-ray structures and 1H NMR spectra recorded in DMSO or DMF. Energy calculation highlights the high flexibility of the ring showing that only 3.1 kJ mol−1 accompanies the conformational change from circular to elliptical. The host–guest bond energy (ΔE) calculated for the Mo12-based clusters is consistent with the experimental stability scale, major variations being due to some constraints undergone by the central alkyl chain.