This study analyzed the coupling between cooking and the subsequent fermentation in fermented legume seed processing. It is, to our knowledge, the first to evaluate how cooking time modulates fermentation. Soybeans were cooked for 10 and 30¿min before being fermented with Rhizopus oligosporus. a-Galactosides, phytic acid, phytase activity, trypsin inhibitors, lectins, and isoflavones were determined during cooking and fermentation. Diffusion into the cooking water was also characterized, and fungal fermentation results were compared with a non-inoculated treatment. Fermentation of seeds cooked for 10¿min resulted in slower mycelial growth and needed to be prolonged to reach a reduction in a-galactosides and an increase in aglycones comparable to those obtained for seeds cooked for 30¿min. Additionally, fermentation with the fungal strain had a low impact on phytic acid in seeds cooked for either 10 or 30¿min. The combination of 10-min cooking and 72-h fermentation of soybeans resulted in a 90% reduction in total a-galactosides, a 17% reduction in phytic acid, and an increase in aglycones to 40¿mg/100¿g DM (dry matter), whereas the combination of 30-min cooking and 48-h fermentation of soybeans resulted in an 84% reduction in total a-galactosides, an 18% reduction in phytic acid, and an increase in aglycones to 39¿mg/100¿g DM. Trypsin inhibitors and lectins remained present in seeds cooked for 10¿min, and R.¿oligosporus could not hydrolyze all the trypsin inhibitors and had no effect on the remaining lectins. This study provides new insights for the fermented legumes food processing sector.