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The aim of this study was to evaluate the effects of soaking and thermal treatment on proteins, anthocyanins, α-galactosides (stachyose, raffinose), tannins and inositol hexaphosphate (IP6), under different conditions, of three Phaseolus vulgaris L. varieties from Madagascar; and evaluate correlation with surface/volume ratio. Overall, dry matter, antinutrients and anthocyanins were impacted by the process, however proteins were not. Depending on varieties and operating conditions, soaking or thermal treatment led to up to 59% losses for dry matter, 73% for tannins, 99% for IP6, 92% for total α-galactosides and 100% for anthocyanins. In certain cases, the process increased dry basis concentration of α-galactosides probably through hydrolysis phenomena from precursors. A positive correlation between the surface/volume ratio of common beans and decrease of tannins and α-galactosides was highlighted. A global antinutritional indicator was used along with the dry matter to evaluate the best conditions to subside all antinutrients and limit the loss of nutrients, combining soaking and thermal treatment. These conditions were soaking (30 C) for 1 h followed by heat treatment at 65 C with 1/5 seed-to-water ratio during 2 h. Appropriate soaking/thermal treatment of common dry bean is crucial to reduce antinutrients and limit nutrient loss. Novelty Impact StatementCommon bean (Phaseolus vulgaris L.) contains antinutrients and oligosaccharides which causes digestive discomfort. Suitable soaking and thermal treatments reduce these compounds and limit the loss of nutrients. As a final product, a common bean partially free of negative compounds could help in processing common beans and be employed as an ingredient in derived product.