A modelling approach was developed to better understand the behavior of the flatulence-causing oligosaccharides in cowpea seeds during isothermal water soaking-cooking process. Concentrations of verbascose, stachyose and raffinose were measured both in the seed and in the soaking water during the process (T = 30, 60 and 95 °C). A reaction-diffusion model was built for the three considered alpha-galactosides both in the seed and in the soaking water, together with a model of water transport in the seed. The model reproduced coupled reaction-diffusion of alpha-galactosides during the soaking-cooking process with a good fit. Produced, diffused and degraded alpha-galactoside fractions were identified by performing a mass balance. During soaking at 30 °C, degradation predominated (maximum found for raffinose degradation rate constant of 3.22 × 10-4 s-1) whereas diffusion predominated at higher temperatures (95 °C).