This study aimed to explore how soy protein isolate (SPI) binds with two types of essential oils (cumin (Cuminum cyminum) (CUM) and coriander (Coriandrum sativum) seed (CO)) and how it affects protein conformation. The results showed that SPI formed stable ternary complexes with CUM and CO that were less than 100 nm in size and had a zeta potential of −15 mV. The successful encapsulation of both CUM and CO within the SPI was confirmed through fourier-transform infrared spectroscopy, X-Ray diffraction analysis, and differential scanning calorimetry tests. These tests showed that both CUM and CO were effectively contained within SPI. The addition of CUM and CO to SPI significantly (p < 0.05) enhanced the ability of small molecules to scavenge ABTS, and this improvement was maintained at a relatively constant level during irradiation for 160 min. These results could be useful in utilizing SPI as an effective co-delivery system for bioactive polyphenol compounds that vary in hydrophobicity and molecular weight.