Soy protein isolate (SPI), including β-conglycinin (7S) and glycinin (11S), generally have low solubility under weakly acidic conditions due to the pH closed to their isoelectric points (pIs), which has limited their application in acidic emulsions. Changing protein pI through modification by esterification could be a feasible way to solve this problem. This study aimed to obtain stable nano-emulsion with antibacterial properties under weakly acidic conditions by changing the pI of soy protein emulsifiers. Herein, the esterified soy protein isolate (MSPI), esterified β-conglycinin (M7S), and esterified glycinin (M11S) proteins were prepared. Then, pI, turbidimetric titration, Fourier transform infrared (FTIR) spectra, intrinsic fluorescence spectra, and emulsifying capacity of esterified protein were discussed. The droplet size, the ζ-potential, the stability, and the antibacterial properties of the esterified protein nano-emulsion were analyzed. The results revealed that the esterified proteins MSPI, M7S, and M11S had pIs, which were measured by ζ-potentials, as pH 10.4, 10.3, and 9.0, respectively, as compared to native proteins. All esterified-protein nano-emulsion samples showed a small mean particle size and good stability under weakly acidic conditions (pH 5.0), which was near the original pI of the soy protein. Moreover, the antibacterial experiments showed that the esterified protein-based nano-emulsion had an inhibitory effect on bacteria at pH 5.0.