Microwave puffing is a process used to obtain low-fat healthy foods by rapid heating of food products to develop high internal pressures in the material that cause significant structural changes. Two-way coupling of complex multiphase transport and large deformations in the material, which is critical to simulate the puffing process accurately, was implemented. A porous media model that includes different phases, solid, liquid water, and gas, and incorporates pressure driven flow and evaporation was used to describe the transport processes in the material. Large deformations were included to model structural changes, with the material treated as hyperelastic. Arbitrary Lagrangian-Eulerian (ALE) framework was used. The model was validated using experimental temperature, moisture, and volume measurement and used to comprehensively understand the puffing process. Uncertainty analysis was carried out to estimate uncertainty in model prediction due to the choice of critical input parameters such as bulk modulus and permeabilities. (C) 2012 American Institute of Chemical Engineers AIChE J, 59: 33-45, 2013