We used a combination of experiments and molecular simulations to investigate at the molecular level the effects of zeolite structure on the adsorption and diffusion of sulfur dioxide, carbon dioxide and carbon monoxide as well as separation processes of their mixtures. Our study involved different zeolite topologies and revealed numerous structure-property trends depending on the temperature and pressure conditions. Sulfur dioxide, which has the strongest interactions with zeolites due to its size and polarity, showed the largest adsorption across investigated temperatures and pressures. Our results indicate that structures with channel-type pore topology and low pore volume are the most promising for selective adsorption of sulfur dioxide over carbon dioxide and carbon monoxide under room conditions, while structures with higher pore volume exhibit better storage capacity at higher pressure. Our results emphasize the need for considering both adsorption and diffusion processes in the selection of the optimal structure for a given separation process. Our findings help to identify the best materials for effective separation processes under realistic operating conditions.