Bambara bean protein is a promising ingredient for further applications in food and non-food industries. In this study, structural changes in Bambara bean protein isolate (BBPI) produced during high pressure processing (HPP) in the 200–600 MPa range at different pH (4.5, 7 and 9) were investigated by fluorescence spectroscopy and molecular modelling. SDS-PAGE analysis indicated that vicilin, a 7S globulin, was the major protein in BBPI. Intrinsic fluorescence analysis at pH 4.5 showed a red-shift when BBPI was treated at high pressure. Phase diagram and quenching experiments demonstrated a third-state model for dissociation of vicilin at pH 9, and existence of four intermediate states when HPP was applied on BBPI at pH 7. Detailed information at atomic level on the structural changes of main proteins from BBPI was provided by molecular modelling. At a glance, HPP resulted in decrease of the total number of hydrogen bonds stabilizing the structure of proteins, which altered exposure of both Tyr and Trp residues. This work is important in development of new food formulations with adequate nutritional and functional properties based on Bambara bean protein.