Novel complexed microgels with enhanced pH and ion stability were constructed using heat-denatured soy protein isolate (SPI) and Chitosan (CS). Their characteristics and their effects on the textural, rheological, and tribological properties of soy yogurt were investigated. The complexed microgels showed larger particle sizes, lower surface hydrophobicity, and higher turbidity than pure SPI microgels. Incorporating the SPI-CS complexed microgels into the yogurts increased their protein content from 3.94% to 5.07% and reduced their fat content from 2.17% to 1.99%. Additionally, incorporating the microgels enhanced the texture of the yogurts, including increased firmness, elasticity, and viscosity, alongside improved water holding capacity (WHC). The incorporation of 0.8% SPI-CS microgels led to the optimum physicochemical characteristics. Rheological analyses demonstrated that incorporating SPI-CS microgels led to an increase in apparent viscosity and shear modulus. Furthermore, the presence of the SPI-CS microgels significantly improved the lubrication properties. Microstructural analysis showed subtle differences in the gel structure of the yogurts after microgel addition. The three-dimensional network structure within the microgel-fortified yogurts was more compact than that in the control. Thus, SPI-CS microgels potentially improve the nutritional profile and quality attributes of plant-based yogurt products.