Human milk (HM) and Infant formula (IF) are assumed to present different digestion kinetics, while rarely directly compared. The study aimed to address this question using a dynamic digestion model (DIDGI®) at the infant stage. Fresh HM (pool from 50 mothers) and standard IF with similar total nitrogen content were digested in triplicate. Digesta were sampled regularly in gastric and intestinal phase from 0 to 180 min to evaluate structural changes (confocal microscopy and laser light scattering), proteolysis (SDS-PAGE and densitometry, OPA), and nitrogen digestibility (µ-Kjeldahl). Differences between groups were assessed using a two-way repeated measures ANOVA. The microstructure of the digesta differed between HM and IF along the gastric digestion. Proteolysis of the common HM and IF proteins, caseins and α-lactalbumin, was significantly slower for HM than for IF. The intestinal degree of proteolysis was lower for HM than IF, at least during the first two hours. Total N digestibility was lower with HM, such as observed in vivo. Peptidomic and lipolysis data will complete the dataset. Despite nutritional similarity, this study highlights the influence of the matrix on the digestion kinetics and gives some further understanding to the global value of digestibility, such as determined in vivo.