Extraframework transition metal ions (TMIs) in zeolites can serve as active sites for adsorption and catalysis. However, due to the complexity and mobility of extraframework cation sites, their applications are significantly limited and the structure-performance relationship is poorly understood. In this Perspective, stable and uniform TMIs in zeolites are exemplified and their characteristics are discussed. A series of TMIs can be introduced to specific cation sites of faujasite via a ligand-protected in situ synthesis route to construct uniform TMIs in the zeolite matrix, namely, TMI@FAU (TMI= Co, Ni, Cu, Rh, and Pt). Coordinatively unsaturated TMIs within faujasite are active for small-molecule adsorption and activation, and therefore, TMI@FAU zeolites show unique properties in adsorption and catalysis. TMI@FAU zeolites appear to be ideal model systems, and the well-defined structure of TMI@FAU greatly facilitates the mechanism studies by spectroscopic investigations and theoretical simulations.