The objectives of this research were to study the effects of several thermal processing methods in connection to water environment on the content of nutrients and non-nutrients (trypsin inhibitors, polyphenols, tannins, phytates and α-galactosides – raffinose and stachyose) in common bean seeds. The processing methods were: (a) soaking in water, 0.1% citric acid, and 0.07% sodium carbonate; all treatments in the temperature ranging from 100°C to 22°C, (b) cooking, (c) autoclaving (1at, 121°C) for 15 and 30 min, and (d) microwave treatment at 1300 and 2000 J/g. Total protein content and trypsin inhibitor activity in dry seeds were, on average, 24.73% d.m. and 29.48 TIU/mg d.m., respectively. The concentrations of polyphenols, tannins and phytates were 2.28 mg/g d.m. (catechin equivalents), 4.39 mg/g d.m. and 19.25 mg/g d.m., respectively. Raffinose and stachyose concentrations were also in dry seeds at level 5.90 and 60.28 mg/g d.m. Soaking of common bean seeds decreased (P < 0.01) the content of tannins. Cooking, autoclaving, and microwave treatment decreased (P < 0.01) the content of trypsin inhibitors, tannins and stachyose; in addition cooking decreased (P < 0.05) raffinose concentration. Alternatively, the above thermal processes had no effect on the concentrations of polyphenols and phytates. In conclusion, the thermal processing may favorably alter (depending on the treatment) the concentrations of bioactive non-nutrients in common bean seeds and retain their expected, functional properties.