Two modelling approaches previously developed and describing separately the diffusion–reaction of folates and alpha-galactosides during cowpea seed soaking, germination and cooking processes were combined here to simulate the effect of some key processing parameters on the nutritional value of cowpea seeds. The simulator was upgraded, considering thermal-pH dependency of both diffusivities and reactivities of folates and alpha-galactosides together with water-to-seed ratio and starch gelatinization. The simulations showed that soaking and cooking processes were deleterious for folates whereas germination promoted the production of folates while reducing alpha-galactosides concentration. This study suggests that a long germination (96 h), followed by a short cooking seems to be optimal both in terms of nutritional value and degree of cooking.