Rh(I)(CO)2 complexes anchored to zeolite HY were converted into Rh4(CO)12 in the zeolite supercages upon exposure to flowing CO + H2O at 35 °C, and the chemistry and kinetics were characterized with infrared spectroscopy. Rh6(CO)16 formed along with Rh4(CO)12, but only in low yield, although it is more stable than Rh4(CO)12. The formation of Rh6(CO)16 was hindered by trapping of Rh4(CO)12 in the supercages and by the low rate of transport of the mononuclear rhodium species. However, exposure of the sample to wet helium at 80 °C caused the Rh4(CO)12 to fragment, generating anchored Rh(I)(CO)2 and also Rh6(CO)16. IR spectra recorded under various conditions led to elucidation of the reaction network for cluster formation and breakup and a strategy of repetitive treatments that boosted the yield of Rh6(CO)16 to >90%. The reversible formation and breakup of the rhodium carbonyl clusters were facilitated by the half-reactions of the water gas shift reaction, with gas-phase products identified by mass spectrometry. The results show how understanding of the reactions within a zeolite allows control of the nuclearity of encaged metal clusters, an important class of catalyst.