The most common hypothesis to explain the influence of food structure on digestion rates is that the proteolysis may be first limited in the stomach by the pepsin activity within the protein structures, as formed during food processing and possibly modified during gastric digestion. It is known that the gastric juice penetrates the food matrix and assists in digestion, but how the acidity and enzyme of the gastric juice affect disintegration of food is still far from being fully understood. There is, indeed, a real lack of methods that allow monitoring the evolution of food micro and nanostructure in the course of digestion. A novel time-lapse synchrotron deep-UV microscopy methodology was developed that made use of the natural tryptophan fluorescence of proteins. It enabled the monitoring in situ of the microstructural changes of protein small gel particles ( 1mm) during simulated gastric digestion. Two dairy gels with an identical composition, but differing by the coagulation mode, were submitted to static in vitro gastric digestion. The kinetics of gel particle breakdown were quantified by image analysis and physico-chemical analyses of digesta. In parallel, the fluorescence recovery after photobleaching (FRAP) technique in confocal microscopy was adapted to investigate the diffusion behaviour of fluorescently labelled pepsin in casein gels of increasing protein concentrations, allowing to form protein networks with different microstructures. The results confirm the tendency of rennet gels, but not acid gels, to form compact protein aggregates under acidic conditions of the stomach. Consequently, the kinetics of proteolysis were much slower for the rennet gel, confirming the hypothesis of a reduced pepsin accessibility to its substrate. Indeed, pepsin diffusivity was quantified (by FRAP) as significantly lower in stronger gels, because of the increasing steric hindrance in the gel microstructure as the protein concentration increased. Moreover, the proteolysis kinetics of the gel particles followed an exponential trend, and while the particle size decreased progressively, their morphology remained unchanged, suggesting that external erosion was the predominant mechanism of the enzymatic breakdown of dairy gels in these experimental conditions.