The synthesis protocols for encapsulation of metal clusters reported here expand the diversity in catalytic chemistries made possible by the ability of microporous solids to select reactants, transition states, and products on the basis of their molecular size. We report a synthesis strategy for the encapsulation of noble metals and their oxides within SOD (Sodalite, 0.28 nm × 0.28 nm), GIS (Gismondine, 0.45 nm × 0.31 nm), and ANA (Analcime, 0.42 nm × 0.16 nm) zeolites. Encapsulation was achieved via direct hydrothermal synthesis for SOD and GIS using metal precursors stabilized by ammonia or organic amine ligands, which prevent their decomposition or precipitation as colloidal hydroxides at the conditions of hydrothermal synthesis (<380 K) and favor interactions between metal precursors and incipient aluminosilicate nuclei during self-assembly of microporous frameworks. The synthesis of ANA requires higher crystallization temperatures (~415 K) and high pH (>12), thereby causing precipitation of even ligand-stabilized metal precursors as hydroxides. As a result, encapsulation was achieved by the recrystallization of metal clusters containing GIS into ANA, which retained these metal clusters within voids throughout the GIS-ANA transformation.