Stable metal-organic frameworks (MOFs) with mesopores (2-50 nm) are promising platforms for immobilizing nanosized functional compounds, such as metal-oxo clusters, metal-sulfide quantum dots, and coordination complexes. However, these species easily decompose under acidic conditions or high temperatures, hindering their in situ encapsulation in stable MOFs, which are usually synthesized under harsh conditions involving excess acid modulators and high temperatures. Herein, we report a route for the room-temperature and acid-modulator-free synthesis of stable mesoporous MOFs and MOF catalysts with acid-sensitive species encapsulated: (1) we initially construct a MOF template by connecting stable Zr6 clusters with labile Cu-bipyridyl moieties; (2) Cu-bipyridyl moieties are subsequently exchanged by organic linkers to afford a stable version of Zr-MOFs; (3) acid-sensitive species, including polyoxometalates (POMs), CdSeS/ZnS quantum dots, and Cu-coordination cages, can be encapsulated in situ into the MOFs during step 1. The room-temperature synthesis allows the isolation of mesoporous MOFs with 8-connected Zr6 clusters and reo topology as kinetic products, which are inaccessible by traditional solvothermal synthesis. Furthermore, acid-sensitive species remain stable, active, and locked within the frameworks during MOF synthesis. We observed high catalytic activity for VX degradation by the POM@Zr-MOF catalysts as a result of the synergy between redox-active POMs and Lewis-acidic Zr sites. The dynamic bond-directed method will accelerate the discovery of large-pore stable MOFs and offer a mild route to avoid the decomposition of catalysts during MOF synthesis.