Soy protein isolate (SPI)–soy isoflavone (SI) complexes were prepared via a pH-driven method at varying SI concentrations (0–7.0 mg/mL) to study their interactions and to analyze the structural and functional characteristics of the complexes. The findings showed that the SPI-SI complexes’ particle size first reduced and then rose with higher SI concentration. Fourier transform infrared spectroscopy revealed a reduction in β-sheet content (35.72%), indicating a limited structural rearrangement toward increased conformational flexibility. Consistently, fluorescence spectroscopy revealed that the fluorescence intensity of SPI diminished with the addition of SI, suggesting hydrogen-bond-mediated interactions. At 3.0 mg/mL SI, the complexes exhibited optimal physicochemical properties, with the most negative zeta potential (−29.78 mV), a solubility increase from 41.90% to 64.70%, and an elevated denaturation temperature from 86.77 °C to 88.79 °C, as well as 1.25-fold higher emulsifying capacity, and 1.86-fold greater emulsion stability; collectively establishing 3.0 mg/mL SI as the concentration where functional advantages are maximized. Overall, these findings demonstrate that pH-induced, non-covalent SPI-SI complexation effectively modulates protein conformation and interfacial properties, providing a green and effective approach for enhancing plant protein functionality in food systems.