The purpose of this research is to screen different processes that could potentially decrease or even eliminate rotenone, a toxic isoflavonoid, from Pachyrhizus seeds. Yam bean seeds have very interesting nutritional characteristics, especially their high protein and lipid contents, and could potentially increase food security in under-nourished populations. However, they contain rotenone, a natural molecule previously used as an insecticide inhibiting the respiratory mitochondrial chain. It was also proven to be toxic to mammals as chronic exposure leads to the development of Parkinson-like symptoms in rats. As the thermosensitivity of rotenone had been reported, this study tested different processes (drying, roasting, boiling, frying, alcohol extraction), tegument removal, and traditional Beninese culinary recipes. Rotenone was then quantified in end-products by a validated method, associating microwave extraction, solid phase extraction (SPE), and HPLC-UV. With these processes a rotenone removal of up to 80% was obtained. The most effective methods were the drying and roasting of the seeds and the maceration of their flour in local alcohol. Rotenone degradation and elimination were confirmed by cytotoxic assays, effectively inducing a decrease in sample toxicity.