Immobilized glucose isomerase is widely used for converting glucose to fructose by enzymatic isomerization. The process takes place in a packed-bed reactor consisting of mesoporous particles with distributed pore sizes and interconnectivities. Its efficiency is, however, significantly affected by deactivation of the mesoporous particles. In this paper, we study deactivation of the mesoporous particles using a three-dimensional pore network model of the pore space with distributed pore sizes and interconnectivities, and investigate several plausible mechanisms of deactivation of the porous particles. The results of the present study, which will be used as the input for simulation of the phenomenon at the reactor level, demonstrates the strong effect of the particles' morphology on the deactivation process.