In the present work, various experimental and theoretical methods were combined to study in detail the modifying effect of differences in the order of deposition of components on the state of silver in bimetallic iron–silver samples based on mordenite. In each of the silver-containing samples, the formation of large (≥2 nm in diameter) varieties of silver was observed, which differed from the varieties in the other samples, and in varying degrees. The formation of large Ag NPs on the outer surface of mordenite is explained by the redox interaction of Ag+-Fe2+ and the selectivity of ion exchange. The local surrounding of Ag in the studied samples is different: for AgMOR—monatomic species dominate, FeAgMOR—silver dimers and AgFeMOR—metal particles. In all investigated samples, the partially charged intra-channel Agnδ+ clusters (~0.7 nm in size) were formed due to partial Ag+ reduction and subsequent Ag0 agglomeration into the mordenite channel. Most of the silver in the bulk of the zeolite is represented in the cationic state attached to the mordenite framework by differently coordinated electrostatic forces, which can be Ag-O, Ag-Si or Ag-Al, with variations in interatomic distances and do not depend on the order of metal deposition. In addition, the arrangement of the cations in the side pockets means that the transport channels of mordenite are free, which is favorable for the application of the materials under study in catalysis and adsorption.