For certain applications, it is useful to control the rate and extent of lipid digestion in different regions of the gastrointestinal tract (GIT) e.g., to control bioavailability, satiety, or blood lipid levels. In the current study, lipid digestion was modulated by mixing two kinds of lipid-loaded biopolymer microgels (alginate beads and carrageenan beads) with different GIT responses. The microgels were formed by mixing lipid droplets with anionic polysaccharide solutions, and then injecting them into a calcium ion solution to cross-link the polysaccharides. Alginate beads remained intact throughout the GIT, leading to a relatively slow digestion rate, whereas carrageenan beads became deformed and dissociated, leading to faster digestion. Experiments using an in vitro GIT model indicated that the rate of lipid digestion could be controlled by mixing alginate microgels with carrageenan microgels. The rate of lipid digestion of the mixed system (1:1) was between that of the two individual systems. These mixed microgel systems may be useful in developing functional foods that modulate lipid blood levels, hormone release, and energy intake.