Zeolites with ordered microporous systems, distinct framework topologies, good spatial nanoconfinement effects, and superior (hydro)thermal stability are an ideal scaffold for planting diverse active metal species, including single sites, clusters, and nanoparticles in the framework and framework-associated sites and extra-framework positions, thus affording the metal-in-zeolite catalysts outstanding activity, unique shape selectivity, and enhanced stability and recyclability in the processes of Brønsted acid-, Lewis acid-, and extra-framework metal-catalyzed reactions. Especially, thanks to the advances in zeolite synthesis and characterization techniques in recent years, zeolite-confined extraframework metal catalysts (denoted as metal@zeolite composites) have experienced rapid development in heterogeneous catalysis, owing to the combination of the merits of both active metal sites and zeolite intrinsic properties. In this review, we will present the recent developments of synthesis strategies for incorporating and tailoring of active metal sites in zeolites and advanced characterization techniques for identification of the location, distribution, and coordination environment of metal species in zeolites. Furthermore, the catalytic applications of metal-in-zeolite catalysts are demonstrated, with an emphasis on the metal@zeolite composites in hydrogenation, dehydrogenation, and oxidation reactions. Finally, we point out the current challenges and future perspectives on precise synthesis, atomic level identification, and practical application of the metal-in-zeolite catalyst system.