In this study, we employed the ultrasound-prepared electrostatic complex and covalent conjugate of soy protein isolate (SPI) and citrus pectin (CP) to prepare β-carotene-loaded nanoemulsions. The in vitro digestion and storage stability of nanoemulsions stabilized by different types of emulsifiers were investigated and compared. Nanoemulsions stabilized by ultrasound-treated complex/conjugate showed the highest encapsulation efficiency; during gastric digestion, these nanoemulsions also demonstrated the smallest droplet sizes and the highest absolute values of zeta potential, indicating that both electrostatic complexation/covalent conjugation and ultrasound treatment could significantly improve the stability of the resulting nanoemulsions. In comparison, complexes were more beneficial for the controlled release of β-carotene; however, the conjugate-stabilized nanoemulsion showed an overall higher bioaccessibility. The results were also confirmed by optical micrographs. Furthermore, nanoemulsions stabilized by ultrasound-prepared complexes/conjugates exhibited the highest stability during 14-day storage at 25 °C. The results suggested that ultrasound-prepared SPI-CP complexes and conjugates had great application potential for the delivery of hydrophobic nutrients.