The effectiveness of the interactions between various alkylammonium cations and the well-defined spherical Keplerate-type {Mo132} capsule has been tracked by 1H DOSY NMR methodology, revealing a strong dependence on the self-diffusion coefficient of the cationic guests balanced between the solvated and the plugging situations. Analysis of the data is fully consistent with a two-site exchange regime involving the 20 independent {Mo9O9} receptors of the capsule. Furthermore, quantitative analysis allowed us to determine the stability constants associated with the plugging process of the pores. Surprisingly, the affinity of the capsule for a series of cationic guests increases continuously with its apolar character, as shown by the significant change of the stability constant from 370 to 6500 for NH4+ and NEt4+, respectively. Such observations, supported by the thermodynamic parameters, evidence that the major factor dictating selectivity in the trapping process is the so-called “hydrophobic effect”. Computational studies, using molecular dynamics simulations, have been carried out in conjunction with the experiments. Analysis of the radial distribution functions g(r) reveals that NH4+ and NMe4+ ions behave differently in the vicinity of the capsule. The NH4+ ions do not exhibit well-defined distributions when in close vicinity. In contrast, the NMe4+ ions displayed sharp distributions related to different scenarios, such as firmly trapped or labile guest facing the {Mo9O9} pores. Together, these experimental and theoretical insights should aid in the exploitation of these giant polyoxometalates in solution for various applications.