Geometric or electronic confinement of guests inside nanoporous hosts promises to deliver unusual catalytic or opto-electronic functionality from existing materials but is challenging to obtain particularly using metastable hosts, such as metal-organic frameworks (MOFs). Reagents (e.g. precursor) may be too large for impregnation and synthesis conditions may also destroy the hosts. Here we use thermodynamic Pourbaix diagrams (favorable redox and pH conditions) to describe a general method for metal-compound guest synthesis by rationally selecting reaction agents and conditions. Specifically we demonstrate a MOF-confined RuO2 catalyst (RuO2@MOF-808-P) with exceptionally high catalytic CO oxidation below 150 °C as compared to the conventionally made SiO2-supported RuO2 (RuO2/SiO2). This can be caused by weaker interactions between CO/O and the MOF-encapsulated RuO2 surface thus avoiding adsorption-induced catalytic surface passivation. We further describe applications of the Pourbaix-enabled guest synthesis (PEGS) strategy with tutorial examples for the general synthesis of arbitrary guests (e.g. metals, oxides, hydroxides, sulfides).