Functional food emulsions enriched in health‐promoting nutrients can help to maintain and improve health and lifestyle. The oil extracted from the Amazonian buriti fruit is renowned for its high levels of carotenoid, vitamin E, and unsaturated fatty acids, which have been linked to improvements in cardiometabolic health. Here, buriti oil in water emulsions are developed and their colloidal transformations are investigated in an advanced digestion model with oral, gastric, and intestinal parts with in situ synchrotron small‐angle X‐ray scattering, cryogenic electron microscopy, and dynamic light scattering under simulated “healthy” and “compromised” digestive conditions. The interior oil phase of whey‐stabilized buriti oil‐in‐water emulsion transforms into highly ordered lyotropic liquid crystalline structures during simulated intestinal digestion at compromised bile conditions. Simulated gastric digestion influences intestinal digestion by slowing it down, resulting in less ordered structures. The digestion‐triggered structure formation is pH‐ and bile salt‐dependent and can be modulated by adding vitamin E to the oil. This tailoring of structures during digestion offers a new pathway to steer digestion kinetics and nutrient bioavailability.