Periodic Density Functional Theory (DFT) calculations were used to determine the preferred localization sites of Fe2+ and Cu2+ exchangeable cations in mordenite zeolite. The results revealed that a single Fe2+ ion preferred to occupy the main channel, whereas Cu2+ ion chosen to inhabit the secondary channel. When both Fe2+ and Cu2+ ions were simultaneously present in the zeolite (bimetallic material), both cations were maximally separated within the unit cell. Notably, the iron cation was embedded in a six-membered ring (6MR) with an α-Fe configuration (FeIIO4 unit), which is observed experimentally in many zeolites; this structure was formed despite the fact that, unlike many other zeolites, in mordenite the 6MR ring contains only one Al ion. Additionally, to evaluate the stability of α-Fe, a hydroxyl radical was introduced into the system to interact directly with the iron ion. The results show that in the absence of Cu2+, iron ion Fe2+ is oxidized to Fe3+. However, when Cu2+ is present in the zeolite framework, the coordination of iron with 6MR is preserved despite the formation of a bond with the hydroxyl radical.