Digestion is a mechanical and chemical process that is only partly understood, and even less so for complex foods. In particular, the issue of the impact of food structure on the digestion process is still unresolved. In this study, the fate of four micronutrient-enriched foods with identical compositions but different microstructures (Custard, Pudding, Sponge cake, Biscuit) was investigated using the 3-phase in vitro model of human digestion developed by the INFOGEST network. Matrix disintegration and hydrolysis of macronutrients (proteins, lipids and carbohydrates) were monitored during the three phases of digestion using biochemical techniques, size-exclusion chromatography, thin-layer chromatography and gas chromatography. Micronutrient release (vitamin B9 and lutein) was monitored using reverse-phase chromatography. Food structure did not greatly influence macronutrient hydrolysis, except for lipolysis that was four-times higher for Biscuit compared to Custard. However, the bioaccessibility of both micronutrients depended on the food structure and on the micronutrient. Vitamin B9 release was faster for Biscuit and Sponge cake during the gastric phase, whereas lutein release was higher for Custard during the intestinal step. Extensive statistical analysis highlighted the impact of food structure on the digestion process, with different digestion pathways depending on the food matrix. It also made it possible to characterise the gastric step as a predominantly macronutrient solubilisation phase, and the intestinal step as a predominantly hydrolysis phase.