SPI/CP conjugates were prepared using ultrasonication of mixed dispersions of soy protein isolate (SPI) and various types of citrus pectin (CP) (LMP, HMP, and LMAP) for 0, 10, 20, 40 and 60 min. Furthermore, the structural features and the transglutaminase (TGase)-induced composite hydrogels performance of SPI/CP conjugates were investigated. Moderate ultrasonication can reduce the particle size from 462.53 to 102.09 nm. Moreover, HMP with high hydrophobic groups (methoxy) was found to be more effective in promoting the unfolding and SPI cross-linking compared to LMP and LMAP. The SPI/HMP conjugate showed a decrease in the total sulfhydryl groups concurrent with an increase in hydrophobicity. The variation of absorption peaks using FT-IR demonstrated that SPI was non-covalently linked with CP to form SPI/CP conjugates via ultrasonic treatment. The CP addition facilitated the conversion of the protein's secondary structure from random coiling to β-sheet. The storage modulus (G′) was higher than the loss modulus (G″), with 20 min ultrasonic treatment found optimum to enhance composite hydrogel rheological properties. The un-ultrasonicated SPI/CP composite hydrogel showed rough surfaces and fragmented disordered structures. Conversely, the ultrasonically treated composite hydrogels showed linear, ordered, and dense microstructures, resulting in improved rheological properties, gel hardness, and water holding capacity. Furthermore, the composite hydrogel protected the survival of Lactiplantibacillus plantarum from gastrointestinal digestion and UV irradiation. These findings suggest that ultrasonication of SPI/CP conjugates can improve the gel properties of TGase-induced composite hydrogels and may be utilized to expand the potential applications of these hydrogels in encapsulation/delivery systems.