While cow and goat milks are used in manufacturing infant formulae (IFs), sheep milk is not allowed in European Union. To assess its suitability, we studied, by a peptidomics approach, the in vitro gastro-intestinal protein digestion of commercial sheep and goat IFs. In both IFs, after 120 min in the stomach, caseins were found massively degraded, while residual whey proteins were detected. In the intestine, β-lactoglobulin, and α-lactalbumin were found resistant to enzymes, particularly in sheep IFs. Compared to goat IF, sheep IF caseins showed a higher degradability, with higher number of released peptides and % protein coverage, particularly for κ- and αs1-casein. On the contrary, whey proteins were found more hydrolysed in goat IF. In the intestine, for both IFs, the peptide profiles resembled those of the stomach, except for α-lactalbumin. Several bioactive peptides were identified, among these casein phosphopeptides. Overall, protein digestion parameters of sheep IF are comparable with goat IF. © 2024 The Authors