Exopolysaccharides produced by lactic acid bacteria are widely used to improve the sensory properties of yogurt. The relation between the physical properties of the microbial exopolysaccharides and the structural and rheological properties of the yogurt are incompletely understood to date. To address this knowledge gap, we studied how two distinct exopolysaccharides influence the microstructure, rheological properties, and syneresis of yogurt. The effect of a negatively charged, capsular exopolysaccharide produced by Streptococcus thermophilus and a neutral, non-capsular exopolysaccharide produced by Lactococcus lactis were investigated. Using quantitative microstructural analysis, we examined yogurt samples prepared with either the capsular or the non-capsular exopolysaccharide, and with mixtures of the two. Confocal laser scanning microscopy and stimulated emission depletion microscopy were employed to visualize the microstructures, revealing differences in pore size distribution, protein domain size, and casein interconnectivity that were not apparent through visual inspection alone. Additionally, variations in rheological properties were observed among the different yogurt types. In the yogurt fermented with both bacterial strains, we observed a combined impact of the two exopolysaccharide types on relevant microstructural and rheological properties. The negatively charged capsular exopolysaccharide enhanced casein interconnectivity and gel stiffness, while the neutral non-capsular exopolysaccharide led to thicker protein domains, an abundance of small pores, and a lower loss tangent. These factors collectively hindered syneresis, resulting in improved structural integrity. Our study not only provides valuable insights into the influence of different exopolysaccharides on yogurt properties, but also presents the first demonstration and quantification of the effect of multiple types of exopolysaccharides on casein interconnectivity. These findings offer guidance for the production of yogurts with customized microstructure, rheological properties, and resistance to syneresis.