This work examines the binding characteristics between the 11S glycinin from soy flour with the aldehyde compound hexanal, at near neutral pH and ambient temperature. FTIR and CD spectroscopy determined that secondary structure changes were evident upon complexation with observed increases in α-helical and unordered structures along with reductions in β-sheets and β-turn structures upon complexation. UV–Vis and MALDI-TOF-MS analysis confirmed the physical nature of hexanal stabilisation, with in silico analysis and fluorescence spectroscopy revealed a low to medium binding strength with a KA range of 3.1 × 102 to 3.1 × 104 M−1 along with a 1:1 binding stoichiometry between the compound and 11S. Molecular docking simulations determined the binding location is situated between chain A and B of the trimer and is largely stabilised by pi-alkyl, hydrogen and van der Waals forces. Findings from this study will provide increased knowledge in the field of flavour compound and protein interactions thus advancing our knowledge of flavour binding and release in plant-based beverage formulations.