The impact of cross-linking chitosan with tripolyphosphate (TPP) on the physical stability and lipase digestibility of chitosan-coated lipid droplets was investigated. Relatively, high TPP levels (≥0.004 wt %) promoted droplet aggregation and gravitational separation, which was attributed to charge neutralization and interdroplet cross-linking. Cross-linked chitosan-coated lipid droplets were formed at lower TPP levels that were relatively small (d ≈ 450 nm), cationic (ζ ≈ +60 mV), and stable to particle aggregation and gravitational separation (pH 3, 21 days). However, these droplets were highly unstable at pH 7 because of a reduction in net particle charge and weakened electrostatic repulsion. An in vitro lipid digestion model was used to study the impact of the chitosan coating on the digestibility of lipid droplets by pancreatic lipase (pH 7, bile salts, pancreatic lipase, and 5.0 mM CaCl2). The rate of lipid digestion decreased when the lipid droplets were coated with chitosan and decreased further when the chitosan coating was cross-linked with TPP. Indeed, both cross-linked and noncross-linked chitosan coatings were able to prevent lipid digestion under conditions simulating the small intestine. This study has important implications for the design of structured emulsions with controlled lipid digestibility and for the targeted delivery of lipophilic functional components to specific regions within the gastrointestinal tract.