The assembly of Ir-4(CO)(12) from Ir(CO)(2)(acac) precursors in the supercages of zeolite NaY was investigated by extended X-ray absorption fine structure (EXAFS) and in-situ infrared (IR) spectroscopies. The data show that the conditions of pretreatment of the zeolite significantly affect the formation process of Ir-4(CO)(12). When the zeolite was initially largely dehydrated, so that the precursor molecules were well dispersed in the zeolite cages, dimeric intermediates in the formation of Ir-4(CO)(12) (approximated as Ir-2(CO)(8)) were observed by both IR and EXAFS spectroscopies. In contrast, when the zeolite initially contained a substantial amount of water, the resultant Ir-4 clusters were formed faster than those in dehydrated zeolite, and evidence of intermediates was not observed. The results show how synthesis in the confined spaces of the zeolite nanopores-in the absence of solvents-affords opportunities to control and elucidate the chemistry, different from that in solution.