New strategies are needed to create high-quality reduced-calorie foods designed to combat the recent rise in overweight and obesity. In this study, we examined the influence of controlled phase separation and gelation of mixed biopolymer systems on the physical properties of model food matrices containing fat droplets, starch granules, and hydrocolloids. Phase separation of pectin–caseinate mixtures was induced through thermodynamic incompatibility (pH7) followed by electrostatic complexation (pH5), and then gelation was induced by adding calcium ions. The resulting model food matrices consisted of fat droplets, starch granules, and a phase separated biopolymer matrix. Confocal microscopy showed that the fat droplets were located within caseinate-rich hydrogel particles, which were present in the interstitial region around the swollen starch granules. All systems exhibited shear-thinning behavior and had yield stresses that increased with increasing biopolymer and calcium concentration. Swollen starch granules had a greater influence on the rheology of the mixed systems than other components due to their relatively high effective volume fractions, whereas fat droplets had a greater influence on the optical properties due to their stronger light scattering efficiency. Calcium ions increased the apparent viscosity of mixed systems, which was attributed to charge screening and ion-bridging effects. These findings suggest that controlled phase separation and gelation of mixed biopolymer systems have potential to create reduced calorie emulsion-based foods, or products with novel textural characteristics.