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Infant formulas (IFs) are used as substitutes for human milk and are mostly based on cow milk proteins. For sustainability reasons, animal protein alternatives in food are increasingly being considered, as plant proteins offer interesting nutritional and functional benefits for the development of innovative IFs. This study aimed to assess how a partial substitution (50%) of dairy proteins with faba bean and pea proteins influenced the digestibility of IFs under simulated dynamic in vitro digestion, which were set up to mimic infant digestion. Pea- and faba bean-based IFs (PIF and FIF, respectively) have led to a faster aggregation than the reference milk-based IF (RIF) in the gastric compartment; that did not affect the digesta microstructure at the end of digestion. The extent of proteolysis was estimated via the hydrolysis degree, which was the highest for FIF (73%) and the lowest for RIF (50%). Finally, it was apparent that in vitro protein digestibility and protein digestibility-corrected amino acid score (PDCAAS)-like scores were similar for RIF and FIF (90% digestibility; 75% PDCAAS), but lower for PIF (75%; 67%). Therefore, this study confirms that faba bean proteins could be a good candidate for partial substitution of whey proteins in IFs from a nutritional point of view, provided that these in vitro results are confirmed in vivo.