Infant formulas (IFs), the only adequate substitute to human milk, are complex matrices that require numerous ingredients and processing steps. Previously, we showed that the quality of the dairy protein ingredients within IFs modulated protein microstructure and in vitro and in vivo digestive kinetics (protein digestion and amino acids plasma concentration). Therefore, the aim was to assess the consequences on gut maturation and microbiota, an important actor within the microbiota-gut-brain axis. Three isonitrogenous IFs were formulated with whey proteins from different origins (cheese whey: IF-A, vs. ideal whey: IFs-B/C) and casein with different organizations (micellar: IFs-A/B, vs. non-micellar: IF-C). Twenty-four Yucatan mini-piglets (2- to 21-day-old), used as an infant model, received one of the three IFs. Digestive contents, faeces, and tissues were analysed using metagenomic, histological, ex vivo permeability and gene expression approaches and a metabolomic analysis was done on serum. Univariate and multivariate statistical analyses were performed. Piglets fed with IF-C had a significantly higher colonic paracellular permeability than those fed with IF-A, which was also associated with a slight immune boost, potentially as the result of increased antigens passage through the gut barrier stimulating the mucosal immune system. Colonic transcellular amino acid transporters were less expressed in piglets fed with IF-C than with IF-A which could be the result of the increased paracellular permeability with IF-C, favouring paracellular transport. These results suggested a combined effect of whey origin and casein supramolecular organization on intestinal physiology in favour of IF-C, whose parameters were closer to those recently reported for human milk-fed piglets (Charton et al., 2022). Even though gut microbiota composition was moderately changed between diets, faecal short-chain fatty acid composition differed according to the whey protein origin, with higher butyrate concentration for ideal whey than for cheese whey. Differences in microbiota fermentative activity may result from differences in digestive kinetics previously observed in vitro between cheese whey-based IF (A) and ideal whey-based IFs (B and C), which could modulate the colonic substrate available for the microbiota. Serum metabolomic analysis showed that tryptophan metabolic pathway was different between IF-A-fed piglets and IF-C-fed piglets with higher serum concentrations of tryptophan, kynurenine and 3-indole acetic acid in IF-C-fed piglets than IF-A, IF-B being intermediate. Seric polyamines, bacterial metabolites from protein digestion, were also more concentrated in piglets fed with IF-C than IF-A. This study suggests that the use of ideal whey and the modulation of casein supramolecular organization are possible avenues to keep improving IFs towards more human milk biomimetics.