The objectives of this research were to study the effects of two biological processing methods, namely solid-state fermentation (using Rhizopus microsporus var. oligosporus sp-T3) and germination on the content of nutrients (protein, fat, ash and carbohydrates) and non-nutrients (trypsin inhibitors, polyphenols, tannins, phytates and α-galactosides – raffinose and stachyose) in common bean seeds (Phaseolus vulgaris L.). Fermentation process had no statistically significant effect (P > 0.05) on gross chemical composition of common bean seeds. However after 5-day germination protein content statistically significant increased (P < 0.05) (from 24.73% d.m in dry seeds to 27.7% d.m.) and content of carbohydrate concentration decreased (P < 0.05) (from 69.7% d.m. to 66.2% d.m.). Solid-state fermentation increased (P < 0.05) polyphenol concentration by 43.4% and decreased (P < 0.01) both trypsin inhibitors (by 100%) and tannins (by 84%). Solid-state fermentation and 5 days germination led to significant elimination of raffinose (P < 0.05) (adequate by 86.3% and 66.4%) and stachyose (P < 0.01) (adequate by 88.4% and 90.3%) in the common bean seeds. In conclusion, the above biological processing methods may favorably alter the concentrations of bioactive non-nutrients in common bean seeds and retain their expected, functional properties.