Abstract Fourier transform infrared (FTIR) method was used to study the conformations of soy protein obtained through aqueous solution and bis(2-ethylhexyl) sodium sulfosuccinate (AOT) reverse micelle extraction. The results showed that there were changes in signal intensity and/or position of IR bands at 4000–400 cm−1 when the soy proteins were separated by two extraction methods. The FTIR spectral changes were subsequently assessed using the second derivative spectroscopy in the amide I region (1700–1600 cm−1). The contents of α-helix, β-sheet, turn and irregular conformations for soy proteins using aqueous solution extraction were 11.6%, 32.8%, 44.3% and 11.3%, respectively; while using AOT reverse micelle extraction 13.1%, 41.6%, 32.5% and 12.9%, respectively. The amount change of these structures might affect functional properties of soy proteins.