Milk proteins have different digestion and absorption kinetics and encrypted bioactive peptides, and thus exert different functionalities. The objective of this study was to evaluate the effect of milk protein composition on physicochemical properties and further physiological responses of a model infant formula when digested in vivo and in vitro. Three formulas with similar nutrient concentration, but different protein compositions were prepared, one containing whey protein (WP) and two others with casein and WP at 40:60 ratio, differing in the β-casein amount. Different β-casein ratios were obtained by performing cold and warm microfiltration on skim milk. Formulas were submitted to a piglet model and a standardized in vitro digestion model. The WP-casein in vivo gastric digesta showed a significantly higher viscosity and modulus compared to WP formula (P<0.05), while no differences were noted in vitro. In both models, a higher aggregated structure was observed for WP-casein digesta, compared to highly fragmented WP digesta. A weaker frequency-dependent gel was observed for the in vitro, compared with the in vivo clots, suggesting different kinetics of these models. Caseins were extensively hydrolyzed to peptides during in vitro gastric digestion, while found largely present in the in vivo coagulum. β-lactoglobulin and α-lactalbumin were resistant to gastric digestion in both models. β-casein level and digestion time did not affect the physical properties and extent of protein hydrolysis of the gastric digesta. Whey protein-casein formulas resulted in higher growth performance, feed intake and feed efficiency in piglets, compared with WP formula. Whey protein formula induced higher plasma GLP-1, confirming the higher satiating effects of these proteins. Whey protein-casein formula promoted a natural pro-inflammatory milieu in piglets, by inducing a higher secretion of the intestinal cytokine TNF-α, with no significant effect of β-casein level. An optimized in vitro cell culture using intestinal Caco-2 cells and LPS stimulated human THP-1 macrophages, showed β-casein may exert anti-inflammatory function, as higher β-casein induced lower secretion of TNF-α and IL-6. The results show that digestion pattern and immunomodulatory functions of a dairy matrix can be regulated by its protein composition, which can be applied in developing matrices with specific health benefits.