The deactivation of Sn-Beta zeolite catalyst during retro-aldolization and isomerization of glucose is investigated. Confocal fluorescence microscopy reveals that retro-aldolization of glucose in CH3OH at 160 °C is accompanied with the build-up of insoluble oligomeric deposits in the micropores, resulting in a rapid catalyst deactivation. These deposits accumulate predominantly in the outer regions of the zeolite crystals, which points to mass transport limitations. Glucose isomerization in water is not only accompanied by the formation of insoluble deposits in the micropores, but also by the structural degradation of the zeolite due to desilication and destannation. Enhanced and sustained catalytic performance can be achieved by using ethanol/water mixtures as the reaction solvent instead of water.