MoS2 and MoO3 have attracted attention due to their interesting properties in energy storage applications, however, the operative charge storage mechanism, whether based on surface ion adsorption and intercalation, is not yet fully understood. In this work, the intercalation of non-hydrated cations into free-standing MoO3-MoS2 electrodes, prepared as composites with graphene, was studied. The oxide material is formed during the solution phase exfoliation process. It is found that tetramethylammonium chloride (TMACl) provides twice the capacitance of tetraethylammonium chloride (TEACl) and tetrapropylammonium chloride (TPACl) solutions. This is attributed to the interlayer spacing of MoS2 (0.615 nm) and MoO3 (0.690 nm), which are greater than the crystallographic diameter of TMA+ (0.558 nm). In contrast, the crystallographic diameter of TEA+ (0.674 nm) and TPA+ (0.758 nm), being larger than the interlayer spacing of MoS2, leads to storage of charge only on the surface of the materials through ion adsorption. Moreover, we have found that use of the TPA+ ion leads to the partial re-exfoliation of the as-prepared materials, which can enhance the capacitance retention during cycling. These results improve the understanding of charge storage mechanism of layered 2D materials.