Zeolites with encapsulated transition metal species are extensively applied in the chemical industry as heterogenous catalysts for favorable kinetic pathways. To elucidate the energetic insights into formation of subnano-sized molybdenum trioxide (MoO₃) encapsulated/confined in zeolite Y (FAU) from constituent oxides, we performed a systematic experimental thermodynamic study using high temperature oxide melt solution calorimetry as the major tool. Specifically, the formation enthalpy of each MoO₃/FAU is less endothermic than corresponding zeolite Y, suggesting enhanced thermodynamic stability. As Si/Al ratio increases, the enthalpies of formation of MoO₃/FAU with identical loading (5 Mo-wt%) tend to be less endothermic, ranging from 61.1 ± 1.8 (Si/Al = 2.9) to 32.8 ± 1.4 kJ/mol TO₂ (Si/Al = 45.6). Coupled with spectroscopic, structural and morphological characterizations, we revealed intricate energetics of MoO₃ – zeolite Y guest – host interactions likely determined by the subtle redox and/or phase evolutions of encapsulated MoO₃.