Metal-loaded zeolites possess metal and solid acid catalysis and therefore can be applied for complex reactions where different reactions proceed on different type of active sites. The optimization of each active sites, such as amount and strength of active sites, are indispensable to improve the yield of the desired product in complex reaction. On the other hand, in metal-loaded zeolite catalysts, the acid site amount is still difficult to be controlled independently because metal particles may be located on the acid sites, leading to the decrease in the acidity. To realize independent control of the each active sites of metal-loaded zeolite, we herein synthesized Rh nanoparticles encapsulated in ZSM-5 catalysts (Rh@ZSM-5) in a water-in-oil microemulsion solution by modifying the synthesis method for metal nanoparticles encapsulated in zeolite in our previous literature. In this method, the formation of metal nanoparticles encapsulated in amorphous silica was followed by the transformation of amorphous silica into zeolite and thus the amounts of solid acid and metal active sites are expected to be controlled independently. Rh@ZSM-5 was found to possess Rh nanoparticles inside of zeolite and the metal particle size and the amount of the solid acid sites were almost independent of the Rh loadings. Reaction of methanol over Rh@ZSM-5 was carried out to elucidate the bifunctional catalysis and its effect on the product selectivity. During the methanol conversion over Rh@ZSM-5, methanol to olefin reaction over solid acid sites and methanol decomposition over Rh metal proceeded in parallel. Rh@ZSM-5 exhibited the larger yield of propylene and butenes than ZSM-5. It could be because that hydrogen atoms produced in situ over Rh@ZSM-5 effectively inhibited the formation of aromatic intermediates to produce ethylene and aromatic compounds.