Noble metal nanostructures are grown inside hollow mesoporous silica microspheres using ship-in-a-bottle growth. Small Au seeds are first introduced into the interior of the hollow microspheres. Au nanorods with synthetically tunable longitudinal plasmon wavelengths and Au nanospheres are obtained through seed-mediated growth within the microspheres. The encapsulated Au nanocrystals are further coated with Pd or Pt shells. The microsphere-encapsulated bimetallic core/shell nanostructures can function as catalysts. They exhibit high catalytic performance and their stability is superior to that of the corresponding unencapsulated core/shell nanostructures in the catalytic oxidation of o-phenylenediamine with hydrogen peroxide. Therefore, these hollow microsphere-encapsulated metal nanostructures are promising as recoverable and efficient catalysts for various liquid-phase catalytic reactions.