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We report here a general synthetic strategy to encapsulate metal clusters within zeolites during their hydrothermal crystallization. Precursors to metal clusters are stabilized against their premature colloidal precipitation as hydroxides during zeolite crystallization using bifunctional (3-mercaptopropyl)trimethoxysilane ligands. Mercapto (−SH) groups in these ligands interact with cationic metal centers, while alkoxysilane moieties form covalent Si−O−Si or Si−O−Al linkages that promote zeolite nucleation around ligated metal precursors. These protocols led to the successful encapsulation of Pt, Pd, Ir, Rh, and Ag clusters within the NaA zeolite, for which small channel apertures (0.41 nm) preclude postsynthesis deposition of metal clusters. Sequential treatments in O₂ and H₂ formed small (∼1 nm) clusters with uniform diameter. Titration of exposed atoms with H₂ or O₂ gave metal dispersions that agree well with mean …