Encapsulation structures for oral administration have been widely employed by the food, personal care, and pharmaceutical industries. Emulsion-filled microgels can be used to encapsulate bioactive compounds, allowing the entrapment of lipid droplets in biopolymer networks and promoting bioactive protection. The influence of pH and biopolymer concentration on the formation and structure of emulsions was evaluated, allowing the production of emulsion-filled hydrogels with potato starch as the main compound, a low alginate concentration, and gelatin in the continuous phase. Potato starch was used because it is generally recognized as safe (GRAS) and has phosphate groups, which allow electrostatic interactions with biopolymers and provide resistance to the network. Emulsion stability was achieved at pH 6, while complexation was verified under acidic conditions, which made the ionic gelation process unfeasible for the production of microgels. After defining the pH for emulsion production, microgels were formed by ionic gelation and coated microgels by electrostatic interactions, as evidenced by quartz crystal microbalance. The alginate and gelatin coating did not affect the morphology of the microparticles. An in vitro digestion assay showed that microgels composed mainly of potato starch were not degraded in the simulated mouth step. The coating layer provided extra microgel protection during digestion, demonstrating the ability of encapsulation systems to promote targeted delivery of bioactive compounds.