There is a growing interest in designing novel food microstructures that can control nutrient digestion and provide satiety for tackling obesity. In this study, phase separated microstructures of skimmed milk powder (SMP) and guar gum (GG) were the main focus, and these can be considered as water-in-water (W/W) emulsions. Through the incorporation of oil into these systems, it was possible to form model systems of SMP-GG-OIL, showing the lipid phase within the protein phase within the polysaccharide phase. The in vitro digestibility of such phase separated model systems of SMP-GG-OIL with different microstructures was investigated using a pH stat method. Confocal laser scanning microscopy also revealed structural changes that occurred to the emulsified lipid droplets as they passed through a gastrointestinal (GI) model. The microstructures were created based on the tie-lines on a previously established phase diagram of SMP-GG, and shown to be able to control lipid digestion. For a selected tie-line, the lipolysis follows the order: protein continuous > bi-continuous > polysaccharide continuous system, at a certain level of oil addition. The mechanism involved in the lipolysis of the designed formulations/microstructures was dependent upon the protein, rather than GG, and was driven by the protein concentration. These findings provide insights for potential applications in functional food designing in the food industry.