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The artificial microenvironments inside coordination cages have gained significant attention for performing enzyme‐like catalytic reactions by facilitating the formation of labile and complex molecules through a "ship‐in‐a‐bottle" approach. Despite many fascinating examples, this approach remains scarcely explored in the context of synthesizing metallic clusters such as polyoxometalates (POMs). The development of innovative approaches to control and influence the speciation of POMs in aqueous solutions would greatly advance their applicability and could ultimately lead to the formation of elusive clusters that cannot be synthesized by using traditional methods. In this study, we employ host–guest stabilization within a coordination cage to enable a novel cavity‐directed synthesis of labile POMs in aqueous solutions under mild conditions. The elusive Lindqvist [M6O19]2− (M=Mo or W) POMs were successfully synthesized at room temperature via the condensation of molybdate or tungstate building blocks within the confined cavity of a robust and water‐soluble Pt6L4(NO3)12 coordination cage. Importantly, the encapsulation of these POMs enhances their stability in water, rendering them efficient catalysts for environmentally friendly and selective sulfoxidation reactions using H2O2 as a green oxidant in a pure aqueous medium. The approach developed in this paper offers a means to synthesize and stabilize the otherwise unstable metal‐oxo clusters in water, which can broaden the scope of their applications. [ABSTRACT FROM AUTHOR]