Zeolite materials have complex structures that can be determined by X-ray diffraction (XRD), but characterizing the nonperiodic defects, the distribution of the aluminum atoms, and the position of the exchanged cations remain a challenge. It was shown that quantum chemistry methods (QMs) are well suited to predict the structure, even with low symmetry. Here, QMs were used to determine the location and coordination of NaI and CuI cations in Si-rich faujasites of Y-type (with moderate Si/Al ratio) and Al-rich faujasites of X-type (Si/Al = 1). Focusing on the first shell of the metal site, we used QM analysis tools to study the various distortions induced by the presence of Al in the rings of faujasites. Such microscopic data were not accessible using experimental XRD methods. In contrast, using the present theoretical approach, it was possible to predict the absence of symmetry at the atomic level and that sites I were not occupied by NaI nor by CuI cations, even for Al-rich faujasites of X-type. The infrared CO probe was used to analyze the interaction of both NaI and CuI with the zeolite framework. Single CO adsorption on NaI and CuI via the carbon atom showed that the calculated νCO stretching frequency bands are mainly upshifted in comparison with isolated CO. The νCO stretching frequency range was predicted to be larger for CuI than that for NaI, and the bandwidth would be affected by different Al distributions in the six-membered rings (6MR): the more the Al atoms in the 6MR, the larger the bandwidth. To gain insights into the metal bonding picture with its neighbors, we performed natural bond orbital (NBO) analysis combined with the quantum theory of atoms in molecules and electron localization function topological analyses (QTAIM and ELF methods, respectively). While it is generally reported that Na cations provide electrostatic interactions with zeolite materials, Cu cations are often assumed to favor covalent interactions. The upshifting of the calculated νCO stretching frequency and our topological analyses rather indicated that the interactions of NaI and CuI with the oxygen atoms of the hosted zeolite were mainly ionic with a weak covalent character in the case of CuI. The adsorption of CO on NaI proceeds via an ionic Na···C interaction, while for CuI, the Cu···CO bond was calculated to be dative with a strong polar character. Whatever the Lewis metal cation, CuI or NaI, the present topological analyses predict that their interactions with the O atoms of the zeolite were ionic.