Using MOFs as size-selection templates, we have for the first time synthesized atom-precise Au11:PPh3 nanoclusters (NCs) and Au13Ag12:PPh3 NCs with high purity by a one-step, in situ reduction method. Specifically, we found that the product released from the frameworks of ZIF-8 is exclusively the Au11:PPh3 NCs rather than polydispersed NCs, and inside MIL-101(Cr) the Au13Ag12:PPh3 NCs constitute the exclusive product. The metal NC@MOF composites are also demonstrated for catalytic application. The high catalytic efficiency for the oxidation of benzyl alcohol indicates that atom-precise noble metal NCs@MOFs may act as a promising class of heterogeneous catalysts. The atom-precise NCs obtained in the MOF templated synthesis imply the future possibility of using MOFs of various pore sizes for the size-selective synthesis of atomically precise NCs. Meanwhile, metal NCs@MOFs will contribute to the understanding of the mechanism of nanocatalyst surface reactions and hence opens up enormous opportunities in heterogeneous catalysis.