The effect of extrusion on the nutritional quality of processed products is vastly unknown. This investigation has explored the possibility of predicting methionine losses in fortified soy‐model systems using a twin‐screw extruder. Since the rate of degradation of methionine has been found to be greatly affected by temperature, mathematical models to describe the extrusion behavior of a system in which sample temperature varies according to location within the extruder and process temperature were established. In this investigation, heat transfer through the barrel wall and frictional heat generated from the rotation of the screws were considered the major factors in determining the actual temperature of the sample. In order to calculate methionine retention during extrusion, it was highly important to determine residence time distribution. the time required for the material to travel through the individual zones of the extruder was of critical importance to accurately predict methionine retention. Mathematical models describing the kinetics of methionine degradation as a function of all parameters and mathematical models describing extrusion behavior were combined to predict the retention of methionine. the simulation was verified by comparing predicted values with experimental data. It was found that the calculated values from this simulation presented the same trends for methionine degradation as those of experimental data with regard to moisture content, protein content, initial methionine concentration and temperature. In general, a reasonable agreement between predicted and experimental values was obtained.