Crossflow microfiltration of mono-dispersed deformable particles of Saccharomyces cerevisiae and Ca-alginate, and rigid PMMA particles was conducted to compare the structure of the flux-limiting layer. The effects of particle deformation due to the frictional drag and mass of the cake, and the area contact among particles on the reduction of porosity were examined to determine how these variations lead to an increase in filtration resistance. The dynamic analysis proposed by Lu and Hwang (AIChE J. 41 (1995) 1443–1455) was modified to examine cake formation during crossflow filtration of deformable particles by taking the transient effect of cake compression and the effect of the area contact between particles into consideration. In situ measurement of filter cake thickness using the infrared reflection method was applied to verify the theoretical results. Both experimental and simulated results showed that the cake formed by deformable particles exhibits a rapid increase in flow resistance or a decrease in local porosity and a high resistant limiting layer is formed next to the filter medium during filtration due to the deformation of particles.