Introduction A major challenge in the next years will consist in producing healthy and sustainable foods with optimized nutritional quality. Food fortification to increase micronutrient intakes is a strategy currently used to overcome deficiencies. Objective Since the structural characteristics of food influence disintegration process during digestion, it appears relevant to assess the impact of food structure on micronutrient bioavailability. Methodology Four model foods have been developed and enriched in lutein and vitamin D. These products were designed such as their composition was identical but their structures and textures were different. Custard, pudding, sponge cake and biscuit were thus produced by modulating the production process. A clinical trial has been set up, involving twelve healthy male subjects for a monocentric, controlled and randomized study, in a cross experimental design. After an overnight fast, kinetics of plasma micronutrient levels were recorded for 8 hours following each product consumption. In a second phase, the model foods have been digested using the INFOGEST in vitro model. Kinetics of matrix disintegration and micronutrients release have been recorded. Main findings The micronutrient absorption curves depended on the matrix. Especially, the biscuit resulted in a significantly later peak of maximal absorption for both micronutrients, and a lower total bioavailability for vitamin D. In vitro, digestion might enable to determine which food characteristics influence matrix disintegration, thereby affecting micronutrient bioaccessibility. Indeed, markers of matrix disintegration, namely proteolysis and lipolysis kinetics, suggested differences amongst the four model foods. Conclusion The in vivo results highlight that food structure modulates the kinetics of micronutrient appearance in plasma. Correspondences might be established between the kinetics of food matrix disintegration during in vitro digestion and the kinetics of micronutrient absorption during the clinical study. Using the DIDGI, a dynamic in vitro digestion model, further studies will aim to refine the quality of the model and the results obtained.