The objective of this paper was to determine the impact of physical factors on the digestibility of proteins isolated from two Polish bean seed species: Phaseolus vulgaris var. Aura and Phaseolus coccineus var. Eureka. The two physical factors were applied during the two hydrothermal treatment processes: autoclaving and microwave cooking. The analysis of the in vitro digestibility of protein preparations, carried out in an environment simulating physiological conditions of proteins digestion in duodenum, showed that temperature and pressure applied during the autoclave cooking significantly improved the digestibility of protein preparations. Contrary to the microwave treatment, after a 10 minute proteolysis cmpleted, the digestibility of protein preparations was lower than the digestibility of protein preparations from bean seeds that had not been thermally treated. On the basis of the SDS-PAGE electrophoresis separation of proteins isolated from native bean seeds prior to the hydro-thermal treatment, it was stated that a fraction showing a mass from 49 to 45 x 103 kDa was predominant; this fraction was identified as a phaseolin which was characterised by a significant thermal stability. In the two processes applied, the physical factors caused changes in the content of protein fractions, in particular in the EA protein preparation. Results of the SDS-PAGE protein separation made the analysis of the in vitro digestibility more complete; they proved that the autoclaving process of bean seeds specifically affected proteins isolated from them; this impact was clearly visible on the presentation of the SDS-PAGE separation.