We produced emulsions by using waxy maize starch nanocrystals (SNCs) (0.075 wt%) and tricaprylin (2.5 wt%) (particle size (D3,2) of the emulsion: 0.5 μm; ζ-potential (ZP): –18 mV at pH 4) and then covered the droplets with chitosan to enhance the emulsion stability under acidic conditions. In the chitosan concentration ranging from 0.1 to 0.4% w/v, the D3,2 of the emulsion increased from 585 to 638 nm and the ZP of the emulsion increased from 40.6 to 47.5 mV, because of thickening of the chitosan-coating layer at the interface. Changes in this thickness affected lipolysis of the emulsions in the in vitro small intestinal environment. The amount of free fatty acids released was 75.0, 64.9, and 56.7% for 0, 0.1, and 0.4% w/v chitosan-coated emulsions, respectively. Additionally, only the emulsions covered with chitosan (0.1–0.4% w/v) were stable for 60 days of storage at pH 4 and 25 °C. The additional chitosan-coating on the emulsions stabilized with the SNCs can serve as a strategy for food hydrocolloids, to enhance colloidal stability under acidic conditions and control digestion in the gastrointestinal tract.